Characters.

[John Grehan]

At 08:42 PM 6/18/04 +0200, pierre deleporte wrote:
>OK you restate your view, but it is simply wrong as cladistics goes. If we 
>have surmounted the semantic problem about "phenetic" (concerns analysis, 
>not characters) and we do agree on what "overall similarity" means (i.e. 
>between taxa, not characters), hence your statement is still wrong.

We will just have to agree to disagree. I view phenetic characters as 
characters that individually represent overall similarity of a feature. To 
me that's phenetic.

>I'm not completely sure what you mean by "limiting characters to..." 
>(still another unusual formulation). But anyway, I interpret it as 
>"putting only potential apomorphies in the data matrix for phylogeny 
>inference". Correct?

Can't remember the context. sorry.

>To put it another way: rooting aside, grouping taxa on "thin enamel" is 
>the same thing as grouping them on "thick enamel" in a cladistic analysis, 
>because all taxa with thick enamel have no thin enamel, and the reverse is 
>true, and we imply that there has been an evolutionary change between thin 
>and thick enamel (the two states). Hence we try to put thick on one side, 
>thin on the other side, and a internal branch between the two. This is not 
>phenetic (this is not % similarity between taxa), this is cladistic 
>optimization of the topology for this character (here, one historical 
>connection between the two states, making thick homologous to thick, and 
>thin homologous to thin). Then you root on thick (state in the outgroups): 
>you get an argument in favor on a tree fitting homology and 
>plesio-apomorphy for this character.

Perhaps. The way I view it is that thin enamel is the outgroup condition - 
whether stated as absence of thick enamel or not, and thick enamel is 
apomorphic within the ingroup being analyzed so I would include thick 
enamel (whether or not one calls that a character state or a character - I 
don't really lose sleep on that one) in the character matrix.

>Cladistic programs do that. Do you ignore this fact?

I don't ignore anything. All I am pointing out in all of this is that if 
you use characters that are not really apmorphies all the algorithmic 
contortions in the world cannot make a cladistic result out of 
non-cladistic data. You seem to have trouble understanding that.

>All this because plesio- versus apomorphy are complementary states of a 
>same character  and not "different characters"

They are different characters in the sense that if thick enamel were not an 
apomorphy for the great apes I would not use it in analyzing human 
relationships.

>You say "real"? You mean your "peculiar" world I guess...

Ha ha.

>"I say you are wrong and I demonstrate it, on pure logical and factual 
>basis, see above. Am I wrong and why?"
>(Not Derridaean, I confess).

Your logic and facts are not pure, they are contextual. That's pure Derrida 
perhaps.

>Why quote a phenetic argument in a cladistic discussion? Cladistic 
>analysis makes no use of autapomorphies. Moving targets and shell games...

It's an arguement that seems to be widely used by paleontologists who 
ascribe to cladistics so its not my problem. Try playng shell games with 
them (which is what it seems like in the quest for someone to give me the 
synapomorphies supporting the human, chimp, and australopithecine clade).

>I don't mean a credo or a vague intuition, I mean that the cladistic 
>programs do not make use of autapomorphies, contrary to your wrong 
>assertion. Will you deny it, and prove your point?

I wasn't saying that they do!

>But yes of course it does if you use a cladistic algorithm! Because the 
>algorithm precisely treats the data to provide the optimal nested set of 
>putative apomorphies. As explained above. Just try and check. You don't 
>seem to want to check what the programs really do. It's very easy, why 
>don't you do it?

Because one would not be using the same data set. To do a cladistic 
analysis I would use a different data set from that proposed in other 
supposedly cladistic analyses because those analyses used characters that 
are not apomorphies (they were treated as if they were apomorphies, but 
they were not).

>And if you find the same result by hand, then you'll have the proof that 
>the program performs cladistic analysis, yes sir, with a data matrix 
>including the putative plesiomorphies

But I would not include plesiomorphies. The problem has been that 
characters are included in data matricies with the claim that they were 
apomorphies when in fact they were not.

>nd thus the data are not treated like in a phenetic analysis; do you 
>really ignore these elementary notions?

No. You seem to be dreaming these things up or misunderstanding what I have 
posted.

>And by the way, stop talking of "potential" apomorphies, just call them 
>"true and definitive" apomorphies.

My choice. You can take yours.


>But the autapomorphic "garbadge" is hopefully ignored by the cladistic 
>program. Yous should know that, be seem to ignore, and on that basis you 
>accuse the cladistic program of being phenetic in this respect, when it is 
>clearly cladistic.

The garbage I am referring to is the use of characters that are being 
accepted as representing apomorphic states when they are not.


>At least in the non-Derridaean world; of course postmodern absolute 
>relativism is another planet, and on this planet you get different logics 
>and different sciences superbly ignoring one another, and everybody is 
>happy in his own peculiar, subjective "real world".

Don't understand any of this.

John Grehan


>Pierre
>
>Pierre Deleporte
>CNRS UMR 6552 - Station Biologique de Paimpont
>F-35380 Paimpont   FRANCE
>Téléphone : 02 99 61 81 66
>Télécopie : 02 99 61 81 88