Fwd: Re: [TAXACOM] Characters.

[John Grehan]

At 07:17 AM 6/23/2004, pierre deleporte wrote:
>A 23:29 20/06/2004 -1100, John Grehan wrote
>
>This acception is a Grehanian exception, and your persistent use of such a 
>personal (unique, indeed) acception of the term impedes the discussion.

Evidently it does not

>Anyway, "overall similarity" of a feature is of no use for distinguishing 
>analyses: phenetic, cladistic, or else. See
>Any character or character state is an apriori hypothesis of "overall 
>similarity", that is simply similarity, of a feature.

I see your view although I do not agree with it.

>The term "overall" makes no particular sense for a character state. How 
>could this statement of similarity be "partial" ? Mystery...

I suppose it is if you look at it that way.

>This is why "phenetic = overall similarity" is applied by everybody (but 
>you) to taxa, not to single character states.

ok

>"Overal" makes sense when you compare series of features in different 
>objects, not when you compare a single feature. This I call 'logic' and 
>useful acception of terms, and this is NOT contextual (see below).

ok - but will still take a different view of this.


>>>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.
>
>The crucial point is not the name you give it, but the evolutionary model 
>than one feature can evolutionarily change into the other feature: enamel 
>can change from thin to thick, or the reverse.

ok. Although the postion I take is that one can make a decision about which 
way a character changes before the analysis and then see how that stands up 
against other characters rather than leaving it entirely up to the analysis 
by leaving the character unordered. Interesting about the evolutionary 
model of one feature changing into another whereas with sequences it seems 
to be a matter of one feature being replaced by another.

>By this very statement you prove that you are ignorant of the fact hat the 
>algorithms do not make use of non-cladistic information in the data,

They do if the data is presented as being cladistic. You seem to have 
trouble getting this basic point. Naturally, as I am the ecccentric one the 
fault in failure of explanation is probably mine.

>condition for supporting a clade, hence the program applies your very 
>cladistic logic, so where is the problem?

The problem would occur only if the character were presented as an 
apomorphy when in actual fact it was not.

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

You're the philosopher.

>OK this si pure post-modernism: if logics is contextual, and if the fact 
>that cladistic programs are not phenetic is contextual, then you win.

If that's they way you want to look at it.

>But fortunately, logic is not contextual. Progress has been made between 
>Aristotle and modern mathematics, but logics is logics and scientists play 
>the game by the sames rules in this respect.

Scientist do use different rules. They are called research programs.



>>>>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!
>
>Of course you did and you persist, you said that if autapomorphies are put 
>into the data matrix, the "contorsions" of the program will not perform a 
>cladistic analysis. You stated this and this is false, as logically 
>demonstrated on Richard's example.

ok I did. This is probably a consequence of my use of a PAUP program from 
some years ago where there was a choice one could make for including or 
exlcuing autapomorphies. I would not use them. Since no one does then


>>>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).
>
>You are simply wrong. The program does not make use of non-cladistic 
>information. The program "reduces" by itself the complete data set to the 
>cladistically informative one. You are ignorant of what the programs do.
>
>>>But I would not include plesiomorphies.
>
>Don't "include" putatively plesiomorphic STATES if you like, but you'll 
>get the same result as the program, which makes no "apomorphic" use of the 
>plesiomorphies you have introduced because it implements the outgroup 
>criterion exactly as you would do by hand.
>
>>>The garbage I am referring to is the use of characters that are being 
>>>accepted as representing apomorphic states when they are not.
>
> From the moment when you put the outgropup in the anaysis, nothing of 
> this kind occurs. Now you can debate on which outgroups should be used, 
> but this has nothing to do with your persisting assertion that cladistic 
> programs perform phenetic analysis (and by the way you throw away all 
> molecular phylogenies, which is not a minor point).
>Here you come back to the case of primates, when the discussion is on your 
>rejection of molecular data on the wrong basis that programs would be 
>phenetic because the data matrix is complete. Which is a complete 
>grehanian mistake, apparently by sheer ignorance of the cladistic algorithms.
>
>>>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.
>
>Thus I translate: your lasting way of using not only highly peculiar 
>definitions (e.g. "phenetic" for qualifying character states instead of 
>taxa) but also pretending that logic and facts are contextual is typically 
>"post-modern". It impedes any rational discussion between people 
>pretending to stand in different "contexts" while dealing with the same 
>topic, and if this attitude is popularized it leads to the end of science 
>and rational debate. Because you'll get several "sciences" and 
>"rationalities" for a same topic (here, phylogeny
>inference) with no possible communication and progress toward common 
>understanding (see more on Richard's web page).
>This is why present post-modernism is the shame of French philosophy (I'm 
>French, no offense), the more in the historical land of the enlightenments 
>which promoted rationality, materialism and universalism, not "contextual 
>logic" promoted by some fashioned text anaysists.
>Now it's not me who quoted Derrida, and thus appealed to postmodernism for 
>talking of science, and pretended that logic is contextual: it's you.
>D'Hollbach preserves, I'm hopefully pre-postmodern...
>
>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