On the topic of @bjmiller’s EN&V post, he writes:
The rarity would then be less than 1/3 to the power of the sequence length. This estimate closely matches the result from Axe’s 2004 β-lactamase experiment that only 1 in 1077 sequences corresponds to a functional fold/domainwithin the protein.
This is a typical impression ID proponents have got from Axe’s work, as that is how it is normally sold to them in the ID literature, which is the idea that Axe has shown the prevalence of any protein with a functional domain(or worse, any functional protein at all), as we can see here: Imagine: 60 Million Proteins in One Cell Working Together
This paper is interesting because it relates to the work of Douglas Axe that resulted in a paper in the Journal of Molecular Biology in 2004. Axe answered questions about this paper earlier this year, and also mentioned it in his recent book Undeniable (p. 54). In the paper, Axe estimated the prevalence of sequences that could fold into a functional shape by random combinations. It was already known that the functional space was a small fraction of sequence space, but Axe put a number on it based on his experience with random changes to an enzyme. He estimated that one in 10^74 sequences of 150 amino acids could fold and thereby perform some function — any function.
But this is of course wrong. Very very wrong. Even Ann Gauger says this is not what Axe has shown, as we can see here:
Doug’s paper showed the rarity of a functional protein with a particular activity (B-lactam) and a particular structure ( TEM-1 B-lactam) (that’s what he and I mean by a functional fold BTW). Out all possible protein structures only 1 in 10^77 will have that structure and that enzymatic activity. It’s a way of answering the question, how many ways are there to make a protein that has that particular structure with that particular chemistry out of all possible proteins.