In article <1992Jul4.231658.6365 at ac.dal.ca> arlin at ac.dal.ca writes:
>Two terminological muddles that warrant clarification:
>>1. PAM stands simply for "percent accepted mutations" and not "point accepted
>mutations per 100 residues," as Gonnet and colleagues suggest (p. 1444, top
>left). I don't know where this interpretation started, but I've seen it many
>times before. Obviously, since "percent" is Latin for "per 100", both
>statements say exactly the same thing-- the only difference is that Dayhoff's
>original coinage conforms smoothly to the acronym "PAM," while the other
>coinage does not.
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I do not care too much about the etymology of "PAM", however I dislike
the use of the term "percent", as people immediately think of a "percentage"
which is now incorrect. It is not a "percentage" of mutated points, else
we could not have 250% !
>>2. But there is a more serious problem with terminology, which may reflect an
>underlying misunderstanding of the evolutionary process (I hope not!). The
>log-odds matrix that appeared in Figure 2 of Gonnet et al. (Science 256: 1444)
>is in no correct sense a "mutation" matrix;
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I explained in an earlier posting that there was an error
in the labelling of this figure.
Gaston H. Gonnet, Informatik, ETH, Zurich.
