More on the 'cladistics' of sequences

[David Williams]

I cannot claim to have read all the posts on this subject but it has been 
with increasing frustration. Reciting what might be known, or assumed, or 
understood has no ultimate bearing on the problem outlined by John Grehan. 
In short, he has a very good point. What, if anything, are the entries in a 
matrix?

Most (all?) of the posts recite issues concerning methodologies, as if the 
solution can ultimately be found in some form of numerical analysis. 
Perhaps this is what leads Pierre, for example, to conclude that “Some 
‘cladists’ effectively rediscovered phenetics (Jaccard index). They belong 
to some trends of the ‘pattern cladistics’ school, which is not 
evolutionary, thus you shouldn't bother if your own goal is phylogeny 
inference”, an assertion based on no evidence or published source, as far 
as I am aware, and entirely of his own making. Efforts to substantiate one 
methodology over another is ultimately pointless. Thus, for example, to 
equate cladistics with parsimony methods is false.

Once we recognise that Cladistics is about relationships, the real 
Cladistic revolution was the reform of palaeontology and that all numerical 
methods are all inherently phenetic (because of the matrix and thus not 
phylogenetic) will we be able to move on.

So
 What, if anything, are the entries in a matrix?

David.