Clades are not classes

[SKÁLA Zdenek]

Pierre, I do not try to offend you; I would only like to separate things that have not much in common:

-----Original Message-----
>>I do not believe that you can place a new property (that was not 
>>observable before) to the set of taxa *after* the analysis to make it class.

>I don't believe that you can forbid anybody to base a classification of 
>living beings on the basis of the results of a previous phylogenetic 
>analysis. The process of phylogeny reconstruction should simply not be 
>confused with the process of classifying on that basis.

Of course - so why are we discussing the class concept? Your taxa are perfect clades (even monophyletic if you want); why to try to interpret them within the class theory? To create distance-based taxa is nothing bad nor unscientific.

>I fear you have a rather naive notion of "observable" properties in biology 
>(and in natural sciences at large). There is no 
>"naturally-obvious-self-evident" properties....

Indeed, but it does not mean that anything goes. What seems to be suspicious to me is to rearrange data matrix by the results of analysis done on just this data matrix. It is not interpretation, IMO, but illegitimate manipulation with the data. Imagine simply what are you doing: cladogram is indicating that character 1 (say flower color) has changed first from -1 to +1 (say, violet-magenta). Then (in taxon A) it changed again (magenta-violet). Now, you are saying that the A has preserved the magenta colour in some respect. I wonder why? It does not make any sense, even within the phylogenetic methodology - the character as such ("flower colour") is something what is homologous through the taxa but the individual character states (violet/magenta) are distributed in distinct regions of the cladogram/groups of taxa. If the ch.state is transformed, its plesiomorphic state is simply missing - this is the base for all cladogram construction and I see no reason why to "recode" characters after analysis. Even your argument that "-1 is a historical avatar of +1" does not change anything - be it "avatar" or not, the +1 is still missing. This argument seems to me to result from a poor distinguishing between the *character* and *character state* (quite frequent mistake in such discussions).

>>  Funnily enough, from the point of view of the class theory, the only 
>> class in the above cladogram is the paraphyletic taxon BCD (supported by 
>> the +1). This can be a case also for other paraphyletic taxa, so it could 
>> be rather dangerous to operate with a class theory to support cladistic 
>> solutions ;-)

>Not at all if you aknowledge the interpretative nature of "scientific 
>observations".

Huh?? The (+1) is a perfect homology common to the (paraphyletic) group BDE; what is bad with this interpretation? On the other side, the reversal (-1) can be viewed as autapomorphy of A. If there would be further taxa-splitting A1+A2 it will be even new synapomorphy. You can imagine it as a transformation series (-1) - (+1) - (++1), say "flowers violet - flowers magenta - flowers white". In such a case and WITHIN THE CLASS THEORY the BDE is indeed a class - it has a unique (and even homologous) character. That this is unacceptable from the CLADISTIC point of view is completely another story.

>The data for phenetics may be 
>interpreted biological similarities (= putative homologies of cladists) but 
>with no attempt to further interpret these similarities in a historically 
>consistent system.

However, we were not discussing the phylogeny reconstruction but classes - I only pointed that "to be a class" will not distinguish between cladistic and phenetic (and eclectic) taxa.

Best!
Zdenek