Bayes & Out-of-Africa vs. Alan Templeton

By Razib Khan | April 26, 2010 8:00 am

Alan Templeton, whose text Population Genetics and Microevolutionary Theory is right below Hartl & Clark in my book, recently published a strongly worded paper, Coherent and incoherent inference in phylogeography and human evolution. The possibility of statistical errors in published work is not shocking, I have heard that when statisticians are asked to sort through papers in medical genetics journals there are elementary errors in ~3/4 of those which have made it beyond peer review. That being said Templeton seems to be making a stronger case than simple refutation of basic errors, in particular he is suggesting that the “ABC” method which lay at the heart of the paper I reviewed last week is incoherent at the root. Here’s Templeton’s abstract:

A hypothesis is nested within a more general hypothesis when it is a special case of the more general hypothesis. Composite hypotheses consist of more than one component, and in many cases different composite hypotheses can share some but not all of these components and hence are overlapping. In statistics, coherent measures of fit of nested and overlapping composite hypotheses are technically those measures that are consistent with the constraints of formal logic. For example, the probability of the nested special case must be less than or equal to the probability of the general model within which the special case is nested. Any statistic that assigns greater probability to the special case is said to be incoherent. An example of incoherence is shown in human evolution, for which the approximate Bayesian computation (ABC) method assigned a probability to a model of human evolution that was a thousand-fold larger than a more general model within which the first model was fully nested. Possible causes of this incoherence are identified, and corrections and restrictions are suggested to make ABC and similar methods coherent. Another coalescent-based method, nested clade phylogeographic analysis, is coherent and also allows the testing of individual components of composite hypotheses, another attribute lacking in ABC and other coalescent-simulation approaches. Incoherence is a highly undesirable property because it means that the inference is mathematically incorrect and formally illogical, and the published incoherent inferences on human evolution that favor the out-of-Africa replacement hypothesis have no statistical or logical validity.

The method which Templeton favors is naturally one which he has pushed in the past. In any case, I don’t know the statistical details well enough to comment with much knowledge, but I see that a statistician has responded to Templeton already, so I would recommend checking that out. I immediately went looking for responses because the paper uses really strong and dismissive language, and I am somewhat wary of that sort of thing when attempting to tear down the fundamentals of a whole field of research (I want to emphasize that overall I enjoy Templeton’s work, but the paper reminded me a bit too much of Jerry Fodor). His citation of Popper in particular seems an appeal to authority that aims to convince the non-statisticians in the audience, and I don’t see the point of that besides rhetorical utility. I do tend to accept somewhat Templeton’s critique of models which assume very little gene flow between hominin populations before the Out-of-Africa migration, though from what I can tell it does seem that Africa has had relatively little back-migration south of the Sahara over the past 50,000 years, so perhaps this is an older dynamic as well. I am cautiously optimistic that DNA extraction from fossils themselves may put to bed some of these arguments over the dance of parameters, though naturally interpretation is always an issue outside of pure mathematics.

For what it’s worth, here’s the model which Templeton’s method favors:

templ

The thin lines represent continuous gene flow between populations, and the thick lines extremely strong demographic & genetic pulses which overwhelm the genetic structure status quo periodically. I have implied something similar as operative on the smaller scale of H. sapiens sapiens.

Citation: Coherent and incoherent inference in phylogeography and human evolution, PNAS 2010 107 (14) 6376-6381; doi:10.1073/pnas.0910647107

  • http://www.gnxp.com p-ter

    whoa, what a bizarre paper. Figure 1 is a Venn diagram of nothing!

    the response you link to gives a lot of good context; it seems like this is one of those cases where a legend in a field find himself a little out of his depth and gets pugnacious…

  • http://haquelebac.wordpress.com/2010/04/06/my-fossil-railroad/ John Emerson

    The possibility of statistical errors in published work is not shocking, I have heard that when statisticians are asked to sort through papers in medical genetics journals there are elementary errors in ~3/4 of those which have made it beyond peer review.

    When I worked in a medical research universisty (OHSU in Oregon) two different friends of mine did statistical work, etc. for researchers. One of them (a sociologist) was amazed at how poorly thought out the biologists’ research programs, experimental designs, statistical understanding, etc. were. the other worked for both psychology and biology researchers, and reported that psychologists were delighted to get any positive correlation at all, no matter how tiny, whereas biologists hoped for strong correlations. The gist of it all seemed to be that people who understood their sciences extremely well would not be good researchers if they hadn’t put any time thinking about these questions.

    The prize was an Ed major elsewhere who was told that he should have some statistics in his paper, so he went to a friend who did statistics and his friend reported to him that his data were opposed to his conclusion. So he got a new statistician.

  • http://www.evoandproud.blogspot.com Peter Frost

    Templeton is arguing that the ‘no admixture’ scenario is a subset of a continuum where archaic humans have contributed to the current gene pool to differing degrees. Therefore, the ‘no admixture’ scenario can never be more probable than all other scenarios taken together.

    This is true if we consider ‘no admixture’ to be an infinitely small point on a continuum of scenarios. An infinitely small point is always smaller than anything else. It’s a bit like the argument that a human can never catch up to a turtle. By the time the human has reached where the turtle was, the latter has already advanced a bit. And by the time the human has reached the turtle’s second position, it has moved on still further.

    Yet humans can outrun turtles. And Templeton’s argument is just sophistry. The ‘no admixture’ scenario is not an infinitely small point. It is compatible with some admixture from archaic humans if such admixture is at trivially low levels. Our genome has some admixture from viruses, yet such gene transfer has never called our humanness into question.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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