Absolutely, I think you and I both agree with the need to be as rigorous as possible in our science here, and be open with the Church about what we do and don’t know, and when we change our views in the light of the evidence.
I have been thinking over the ARGweaver paper since you clarified for me what the authors were doing. My initial mis-understanding of the paper made me think that different assumptions about population sizes could be a game-change for your calculations of TMR4A, but now I understand the paper better I don’t think this is the case. Thank you for helping me on that one. This was the most major of my criticisms, and now that this is removed I feel more confident in your conclusions.
As you have said, this is just a first attempt at an estimate of TMR4A, and a more rigorous approach would be possible, but would be a lot of work. As we have also noted, the results could be affected by revisions in the estimation of recombination rates and mutation rates. It could also be that if the phylogenetic trees were built in a way which sought to maximise the number of mutations in the first four diverging lineages, different topologies might emerge (I’m not sure about this, but it would be interesting to examine the possibility). Unexpected factors that we have not accounted for as yet could also come into play, as happened in the Lenski experiment in a very different context. We can never be completely sure, as science is always progressing.
However, despite this, the big picture is that I am very much in agreement with you, and it is probably not profitable at this stage to continue to belabour criticisms of your analysis.
I think at this stage, it would be helpful to the Church if we could come up with a statement that we can all agree on, that summarises where we have come to in this discussion. This has been a long discussion that many will not have the time to wade through, and if you, @DennisVenema and perhaps @glipsnort and I, could come up with a statement that summarises the degree of consensus that we are reaching, then that might be helpful to the Church at large.
From my reading of our discussion, though there are things that we still differ over, here is a statement that I think we could all agree on:
As Christian biologists, we have over the last few months reviewed the population genetic literature, asking if it is possible that all modern humans could descend from a single couple within a theistic evolution (or evolutionary creation) framework. We have assumed that humans share common ancestry with apes, and that God has not intervened with physical miracles. Our task has been difficult because the hypothesis of a bottleneck of two in the human lineage has not been directly addressed in the scientific literature using genome-wide human diversity data. Nonetheless, from those published studies of human diversity that we have reviewed, and based on our understanding of current theory, we have drawn tentative conclusions. We conclude that current human genetic diversity data does not rule out a bottleneck of two individuals in the human lineage between approximately 400,000 and 7,000,000 years ago, but neither do they show that such a bottleneck has happened. Current analyses and models suggest that a two-person bottleneck has not occurred below a threshold of approximately 400,000 years before present. More research is needed in this area, and we are open to new analyses moving this threshold up or down.
If @swamidass @DennisVenema and perhaps @glipsnort agree that this is a consensus we have reached, I suggest that we publicly affirm this. I am very happy to discuss modifications to this statement that would enable all of us to affirm it.