What Steve is trying to communicate to you is that in small populations, natural selection is pretty much not a factor. Genetic drift (i.e. non-selected changes in allele frequencies) predominates.
Also, sometimes natural selection at a certain locus might favour multiple alleles (inflating Ne) or favour only one allele above all others (and thereby reduce Ne). That’s why these methods prefer sequences that are not under natural selection (which is most of the genome, fortunately).
I’m not arguing that current methods are infallible. I’m making the (rather obvious) observation that if we continue to find new genetic variation in human populations, we will accordingly increase our estimate of Ne. You’re correct that it is formally possible that we will find out in the future that our methods are inaccurate. That is a possibility for any scientific endeavour. The fact that several different methods with different assumptions return estimates that agree with each other gives us confidence that this won’t happen. Much more likely is that we will continue to refine our models, and collect more data. I strongly suspect that this will continue to increase our estimate of Ne up until the point where we have adequately surveyed sub-Saharan Africa. YMMV.
Let me assure you that I know very very well that I am the one learning most by far from this exchange. This topic is, after all, very far from my own area of scientific expertise. A very small part of my aim was to back up previous claims that the objectivity of scientific discovery comes from the fact that it consists of procedures anyone can follow to get the same result – it really isn’t about positions of authority. If we are determined enough we can investigate and find the facts of these things ourselves. So you have my appreciation for taking time with me in this.
At this point, I think any objections I might continue with are reduced to the level of nitpicking. Including the slightly different prediction that I would make for where things will go from here. I certainly look forward to new developments in the near future.
Can I ask what you are predicting, and what you are basing that prediction on? I’m curious.
Its basically what I have already said. It just seems to me that the repeating pattern is that we keep finding out that things are considerably more complicated than we originally thought. And that with all that data to be explored, this one analysis isn’t likely to be the end of the way in which we can extract information of out it about the past.
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