Fwd: Re: [TAXACOM] Characters.
pierre.deleporte at UNIV-RENNES1.FR
Wed Jun 23 13:17:41 CDT 2004
A 23:29 20/06/2004 -1100, John Grehan wrote
>>At 08:42 PM 6/18/04 +0200, pierre deleporte wrote:
>>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.
This acception is a Grehanian exception, and your persistent use of such a
personal (unique, indeed) acception of the term impedes the discussion.
Anyway, "overall similarity" of a feature is of no use for distinguishing
analyses: phenetic, cladistic, or else. See Richard Jensens's data matrix
Any character or character state is an apriori hypothesis of "overall
similarity", that is simply similarity, of a feature. The term "overall"
makes no particular sense for a character state. How could this statement
of similarity be "partial" ? Mystery...
This is why "phenetic = overall similarity" is applied by everybody (but
you) to taxa, not to single character states.
"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).
>>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.
The other crucial point is that the program will not support clades by
symplesiomorphies, even if you put them in the data matrix, because the
progeram is cladistic, not phenetic.
>>I don't ignore anything. All I am pointing out in all of this is that if
>>you use characters that are not really apomorphies all the algorithmic
>>contortions in the world cannot make a cladistic result out of
>>non-cladistic data. You seem to have trouble understanding that.
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, even
if you put "everything" into the data matrix. It is not because you give
the complete data matrix thatthe program will make use of all of it without
discrimination. Programs do not perform "contortions", they implement the
cladistic logic. They have been devised by cladists for performing
cladistic analysis. Not phenetic analysis. You obviously ignore that (and
apparently don't want to learn).
>>> if thick enamel were not an apomorphy for the great apes I would not
>>> use it in analyzing human relationships.
Neither would the program, despite the fact that you put both states in the
data matrix, because the program will root on the outgroup state, and thus
use only the apomorphic
condition for supporting a clade, hence the program applies your very
cladistic logic, so where is the problem?
>>Your logic and facts are not pure, they are contextual. That's pure
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. Note
that you will always win. You can indefinitely play the game of developing
a pseudo-discusssion, and always pretend that you're applying "your own
contextual logic and reality of facts" (not only your own peculiar
definitions, which are a great burden in the discussion, but can be
overcome with some good will). And if so, science is dead, as Richard
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.
Not post-modern people of course: they like taking postures in different,
pretendedly incommensurable contexts.
And cladistic programs perform cladistic analysis anyway you take them.
But a strict post-modernist may not care at all and pretend that logic is
plural and incommensurable and that the fact does not exist in his own context.
>>>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.
>>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
>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...
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