Gentlemen, I see my name has been mentioned here. I’m a bit overwhelmed by work, so cannot participate in this discussion, but I do want to make a few clarifying points regarding my own thinking on this problem.
First, as I have stated previously, the quality of any estimation depends upon sufficient sampling, and I greatly doubt that we have sufficient data to estimate the FI required for any protein in a specific species. The same probably goes for genus, and maybe even for family and order. My interest has always been, and continues to be, the FI required for the origin of novel protein families, rather than for a protein in a single species or genus.
For this reason, I have focussed, and continue to focus on protein families that have had the benefit of sufficient sampling produced by thousands of independently evolving populations across a wide range of taxa (preferably across many phyla). In discussions with various people in the field, there seems to be two research questions to answer (which appear to have come up here, though I’ve not read anything other than gpuccio’s one reply included in the email sent to me):
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How can we test for sufficient sampling, given common descent and,
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How can we test for sufficient sampling, given the possibility of a global maximum fitness in sequence space, clustering our data in only a subsection of sequence space?
For the past 8 months or so I have been working on a method to provide answers to both questions. The method itself was not difficult, but the testing of that method has been time consuming. I cannot discuss anything related to this here, as I am submitting my findings to a journal for peer review and publication. I will say this, however … I wouldn’t even think about estimating the FI for a protein from the data for an individual species (e.g., human), for obvious reasons when one scans the sampling available at present. But my initial assumptions several years ago regarding sampling broadly across phyla or kingdoms is being verified to produce reasonably accurate estimates of FI required for the origin of many protein families.
I can’t say anymore until the paper passes review and is published. The input and critiques I’ve had thus far from a few non-ID scientists sceptical of ID, has been especially valuable, but I cannot widen the circle of discussion any further until after the paper is out. As my former supervisor urged me … “stop leaking your research and focus on submitting more papers for publication.”
As I indicated at the outset, I cannot participate in this discussion, although it does look to be interesting.