I’ve been running the African Ancestry Project for a while now on the side on Facebook. But it’s getting unwieldy, so I finally set up the website. The main reason I started it up is that there have been complaints for a while now of problems with the 23andMe “ancestry painting” and such for some African groups. For example, a Nubian might be 70% “European.” One might argue that this is due to Arab admixture, but this is clearly not so if you look at the PCA plot. What’s going on? Probably a problem with the reference populations (only Yoruba for Africa), ascertainment bias in the chip (they’re tuned to European variation), and the fact that African genetic variance can cause some issues. I don’t know. But the problem has been persistent, and since most of the other genome blogging projects exclude Africans because they’re so genetically diverse I decided to take it on.
Three groups of people have submitted:
- People of the African Diaspora in the New World
- People from Africa, disproportionately Northeast Africans (Horn of African + Nubia, etc.)
- People of some suspected or known minor component of African ancestry
I’m at ~70 participants now. As one reference population set I’ve been using a subset of Henn et al. as well as some populations from Behar et al. I call this my “thin” set since there are only ~40,000 SNPs. A “thick” set has on the order of 300-400 thousand markers. But fewer populations. I’ve been putting the AAP members through ADMIXTURE in batches of 10, but I also run them all together sometimes for apples-to-apples comparisons. Yesterday I ran AF001 to AF070 from K = 2 to K = 14, unsupervised, with the thin reference. If you want to see all the results, go here. Doing all this myself over and over has given me some intuition as to the pitfalls in this sort of analysis. Especially in the area of confirmation bias.
This morning I received an email from the communication director of the American Anthropology Association. The contents are on the web:
AAA Responds to Public Controversy Over Science in Anthropology
Some recent media coverage, including an article in the New York Times, has portrayed anthropology as divided between those who practice it as a science and those who do not, and has given the mistaken impression that the American Anthropological Association (AAA) Executive Board believes that science no longer has a place in anthropology. On the contrary, the Executive Board recognizes and endorses the crucial place of the scientific method in much anthropological research. To clarify its position the Executive Board is publicly releasing the document “What Is Anthropology?” that was, together with the new Long-Range Plan, approved at the AAA’s annual meeting last month.
The “What Is Anthropology?” statement says, “to understand the full sweep and complexity of cultures across all of human history, anthropology draws and builds upon knowledge from the social and biological sciences as well as the humanities and physical sciences. A central concern of anthropologists is the application of knowledge to the solution of human problems.” Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.
Changes to the AAA’s Long Range Plan have been taken out of context and blown out of proportion in recent media coverage. In approving the changes, it was never the Board’s intention to signal a break with the scientific foundations of anthropology – as the “What is Anthropology?” document approved at the same meeting demonstrates. Further, the long range plan constitutes a planning document which is pending comments from the AAA membership before it is finalized.
Anthropologists have made some of their most powerful contributions to the public understanding of humankind when scientific and humanistic perspectives are fused. A case in point in the AAA’s $4.5 million exhibit, “RACE: Are We So Different?” The exhibit, and its associated website at www.understandingRACE.org, was developed by a team of anthropologists drawing on knowledge from the social and biological sciences and humanities. Science lays bare popular myths that races are distinct biological entities and that sickle cell, for example, is an African-American disease. Knowledge derived from the humanities helps to explain why “race” became such a powerful social concept despite its lack of scientific grounding. The widely acclaimed exhibit “shows the critical power of anthropology when its diverse traditions of knowledge are harnessed together,” said Leith Mullings, AAA’s President-Elect and the Chair of the newly constituted Long-Range Planning Committee.
Chemistry likes to think of itself as the “central science.” Is that true? Intuitively it makes sense. But how can we measure that more rigorously? In comes the Stanford Dissertation Browser:
The Stanford Dissertation Browser is an experimental interface for document collections that enables richer interaction than search. Stanford’s PhD dissertation abstracts from 1993-2008 are presented through the lens of a text model that distills high-level similarity and word usage patterns in the data. You’ll see each Stanford department as a circle, colored by school and sized by the number of PhD students graduating from that department.
When you click a department, it becomes the focus of the browser and every other department moves to show its relative similarity to the centered department. The similarity scores are computed using a supervised mixture model based on Labeled LDA: every dissertation is taken as a weighted mixture of a unigram language model associated with every Stanford department. This lets us infer, that, say, dissertation X is 60% computer science, 20% physics, and so on. These scores are averaged within a department to compute department-level statistics (the similarities shown), and need not be symmetric. For instance, Economics dissertations at Stanford use more words from Political Science than vice versa. Essentially, the visualization shows word overlap between departments measured by letting the dissertations in one department borrow words from another department. Which departments borrow the most words from which others? The statistics are computed for each year in the data.
You can play around with the browser here. I’m assuming at some point in the near future this sort of analysis is going to get much, much, easier, because of the sea of data which powerful software can extract and visualize patterns out of. Below are the fold are five screen shots I thought were of interest. Genetics, biology, and chemistry dissertations in 2008. And Anthropology in 2007 and 1998.
David Dobbs has a link roundup and commentary on what’s been going down with l’affaire Hauser. It doesn’t look good for Hauser et al., though it seems that the downfall was precipitated ultimately from within if press reports are to be believed. Part of the issue here seems to be that there’s a level of opacity in the scientific process, and you have to trust the scientists themselves over the short term. Over the long term the system of science and its general culture tends to self-correct, at least in the natural sciences, but over the long term careers can rise and fall, and science is produced by human beings. We know that science is possible, it’s been done for at least a few centuries even with the most constrained definitions, but we also know that it isn’t necessarily entailed by the existence of any complex society. A particular set of contingent conditions need to come together to allow for its emergence and perpetuation. So it’s all fine and good to observe that science as a system self-corrects, but without the individual incentives and institutional checks & balances it may never have a chance to flower.
This brings me to Dobbs’ comment about more “open science”:
Are Top Scientists Really So Atheistic? Look at the Data asks Chris Mooney. He’s referring to a new book, Science vs Religion: What Scientists Really Think by Elaine Howard Ecklund. Here’s the Amazon description:
… In Science vs Religion, Elaine Howard Ecklund investigates this unexamined assumption in the first systematic study of what scientists actually think and feel about religion. Ecklund surveyed nearly 1700 scientists, interviewed 275 of them, and centers the book around vivid portraits of 10 representative men and women working in the physical and social sciences at top American research universities. She finds that most of what we believe about the faith lives of elite scientists is wrong. Nearly 50 percent of them are religious. Many others are what she calls “spiritual entrepreneurs,” seeking creative ways to work with the tensions between science and faith outside the constraints of traditional religion. Her respondents run the gamut from Margaret, a chemist who teaches a Sunday-school class, to Arik, a physicist who chose not to believe in God well before he decided to become a scientist. Only a small minority are actively hostile to religion….
Some of Chris’ readers are rather agitated about this all, and he suggests that perhaps they should read the book to answer their questions. I haven’t read the book, but you can read much of it on Google Books or Amazon’s text search feature. Skimming a bit I encountered the term “spiritual atheist,” which many might find an oxymoron. Rather than present her interpretation, let me post some of the tables which have data in them.