What is wrong with some ancestry testing

This is an example of the type of question I receive all the time:

Here is some genetic analysis of Somalis from yours truly. I don’t necessarily blame the public here, as the marketing of Y and mtDNA lineages has really gotten out of control recently. The problem is that the fine print that Y and mtDNA follow only one direct line of descent is usually there. But, it is accompanied by rich visual and narrative media that tells a story about that marker, and it is this that is salient for most. Not that the story being told is only a very small part of the overall epic cycle that is your genealogy.

(Also, in population genetics using the word “Caucasian” is really confusing. G2 can often be thought of as a Caucasian haplogroup, but I don’t think that that’s what my correspondent meant)

The full shape of human history

With great ambition comes the opportunity for stupendous failure. If one does not strive, one can not fail in a bold manner. And Ian Morris is bold indeed. I read his previous book, , and found in enjoyable. And yet it isn’t that original a departure from many economic histories one might encounter. This is a major worry I have with Morris’ new book, . Is there anything here that Angus Maddison fans will find novel?

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The unstylized science of human culture

I encountered Joe Henrich’s work about 10 years ago. As a fellow traveler of Robert Boyd, and admired by Dan Sperber, none of this is coincidental. These are the sorts of cultural anthropologists who I can understand in my bones. Benearth the jargon there is no attempt at signalling artifice. For a taste of Henrich’s research, see the anthology . For those who prefer more theoretical heft, will satisfy you ( is a popularized condensed form of this book).

If you haven’t heard of Henrich & his colleagues, you’ve heard of their work. They’re behind the popularization of W.E.I.R.D., “Western, Educated, Industrialised, Rich and Democratic.” The concept refers to the fact that much of psychology consists of observations and experiments on exactly such populations, and then extrapolation from those results to make general assertions as to the character of human nature. This is a very popular and widely known idea that crops up in everyday conversation. I’ve been patronizingly lectured about it numerous times by individuals who perceive that I’m being too insensitive about some barbarous cultural practice (in my personal communication I don’t make it a secrete that I prefer small-l liberal Western values; there’s no shame in W.E.I.R.D.ness). Speaking of insensitivity it seems Henrich was accused of exactly such early on in his career by the usual suspects:

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Science is hard, but it is possible

Again, Chagnon, Sahlins, and science:

When we allow personal ideological bias rule to our scholarly work, we limit the value of our research to answer real questions and to contribute to broader social and scientific debates. If you have an ideological axe to grind, either leave scholarship and go into politics, or else find ways to achieve a level of scholarly objectivity in your research and writing. (yeah, I know, the postmodernists are going to smirk about how naive I am to even use the word “objectivity.” Check out my past posts on epistemology; one can employ objective methods and maintain an overall level of objectivity while admitting that the world is messy and researchers are never free of preconceptions or bias.).

To paraphrase John Hawks, “I think its time to reclaim the name ‘archaeology” from past generations.” We have lots of data and ideas to contribute to major scholarly and public debates today, but too often our writing and epistemological stance work against any wider relevance.

For various reasons cool detachment is harder in anthropology, nor should it always be employed. But the pretense and striving for detachment is an essential part of science (coupled with curiosity and passion about the subject of interest). A counterpoint can be found in the comments below:

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The abuse of ancestry testing is bad for personal genomics

I have very little with which I can disagree with in this Mark Thomas piece, To claim someone has ‘Viking ancestors’ is no better than astrology. His conclusion:

Exaggerated claims from the consumer ancestry industry can also undermine the results of serious research about human genetic history, which is cautiously and slowly building up a clearer picture of the human past for all of us.

Many of the commercial companies plant stories in the media that sound exciting and seem scientific. But very often they are trivial or wrong, are not published in peer-reviewed scientific journals, and just serve as disguised PR for the company.

The only caveat I would offer is that the sort of confusions and misrepresentations that occur with Y and mtDNA phylogeography are dampened when you are looking at a million markers throughout the whole genome. This does not mean there are still no confusions and misrepresentations (e.g., the reference populations matter a great deal when you present someone as a linear combination of X populations, and that summary is still not reality as such, but an informative model). One alarming aspect of the trade in Y and mtDNA is that I’ve met several people who somehow believe that only these lineages are ancestrally informative. That is probably a function of the ease with which you can say someone is “descended from Niall of the Nine Hostages.”

Addendum: I actually asked Jim Wilson on Twitter if I could get a look at the raw results (not even raw data) for the claims made. One major problem when scientists have a go-to-media-first strategy is that things get out of hand very quickly.

What is the good life?

Now that I have a daughter I do reflect a bit more on what the purpose of my life is, because at some point I want to talk to her about the purpose of her life. There is a little bit of irony in this insofar as now she is a primary purpose of my life! But in any case, though raison d’être speaks to me, additionally my job is also to make sure that my daughter doesn’t become a C.P.A. Certain professions, such as dentistry or accountancy, are honorable. But there are enough people who want to enter those financially lucrative professions as it is. In a world of such absolute affluence we can afford the luxury of the life the mind. Aristotle’s father was a physician, no doubt a good man. But his memory persists only because of the incandescent brilliance of his son, who ventured into wide intellectual waters.

Speaking of Aristotle, Aristotle Onassis is reputed to have said that “If women didn’t exist, all the money in the world would have no meaning.” Point taken, and I think there’s a great deal of truth in this. But let me rephrase it: if books didn’t exist, all the time in the world would have no meaning. To many this sort of assertion would seem strange, but I suspect among my readership it is comprehensible. And by books I don’t mean to imply paper and ink and binding, I mean the information encoded within those books.

With that out of the way, I thought I would share an email from a long time reader (though only very rarely a correspondent). I don’t necessarily agree with everything stated here obviously, and I hope that the comments don’t devolve in discussions of the nature of East Asian society. I didn’t feel comfortable expurgating that aspect just because some might take objection though. Rather, it is to consider how one might find a place to flourish and be nurtured socially in their intellectual explorations.

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Noble Savages, right method, wrong results, right enemies

I read , Napoleon Chagnon‘s memoir, last week. There isn’t much to say about this book that’s revelatory, but it definitely was a page turner. As far as my personal tastes go there was a little too much autobiography, and not enough science, in  . But it’s a long work, so in absolute terms there’s a lot of science to dig into if you want to skim over the personal sections (frankly, I had a hard time keeping all the various tribes and individuals straight). There have been many reviews of  since it came out last week.  If you haven’t read the profile in The New York Time Magazine, I advise you to do so right now. At Scientific American John Horgan put up a post which illustrates how Chagnon has become a sort of token in the tribal wars between scientists (or scientists and no-scientists). You can see this in two reviews at The New York Times, one which consists of an extended sneer from a professor of cultural anthropology and gender studies, Elizabeth Povinelli, while the second treatment from Nicholas Wade reads almost as a panegyric. Charles C. Mann navigates the middle path in his review, being critical in some instances, but by and large praising the memoir.

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Michael Eisen wants peer review comments on his paper

This is great, Please review our new paper: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression:

It’s no secret to people who read this blog that I hate the way scientific publishing works today. Most of my efforts in this domain have focused on removing barriers to the access and reuse of published papers. But there are other things that are broken with the way scientists communicate with each other, and chief amongst them is pre-publication peer review. I’ve written about this before, and won’t rehash the arguments here, save to say that I think we should publish first, and then review. But one could argue that I haven’t really practiced what I preach, as all of my lab’s papers have gone through peer review before they were published.

No more. From now on we are going to post all of our papers online when we feel they’re ready to share – before they go to a journal. We’ll then solicit comments from our colleagues and use them to improve the work prior to formal publication. Physicists and mathematicians have been doing this for decades, as have an increasing number of biologists. It’s time for this to become standard practice.

Some ground rules. I will not filter comments except to remove obvious spam. You are welcome to post comments under your name or under a pseudonym – I will not reveal anyone’s identity – but I urge you to use your real name as I think we should have fully open peer review in science.

OK. Now for the paper, which is posted on arxiv and can be linked to, cited there. We also have a copy here, in case you’re having trouble with figures on arXiv.

Peter A. Combs and Michael B. Eisen (2013). Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. 

Please leave comments on Eisen’s post.

Via Haldane’s Sieve.

The age of non-invasive pre-natal testing is here

Last summer Neuroskeptic posted on The Coming Age of Fetal Genomics. It seems likely to me that this “age” won’t be ushered in with a bang, but we’ll be there before we know it. After all, most people aren’t thinking about having children at any given moment, and don’t track biomedical advances in genetic disease screening until they’re crossing that bridge. Over at Xconomy Luke Timmerman has a post up, Natera Joins Quest in Four-Way Battle for Prenatal Genetic Tests. Here are some important details:

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