[Taxacom] DNA homologies

[pierre deleporte]

At 12:16 28/09/2006 -0400, John Grehan wrote:

>or your argument is too poorly constructed to lead me to a different view. 
>Such things always happen in science and it eventually comes out in the wash.

OK let's try and wash

>As before, they can claim the studies are cladistic because they put the 
>characters through a cladistic algorithm.

exercise : overlooking esoteric jargon, consider Grehan's phylogenetic 
"algorithm" below (source: Taxacom list):

- use prior compatibility analysis to select putatively uniquely derived 
characters to constitute the data matrix, call them "cladistic" characters 
(any other kind is to be called "phenetic")
- make an exception to this rule when the characters support the group 
(Homo, Pongo) (e.g.: ischial callosities and enamel thickness)
- treat the data set itself with standard cladistic analysis, not 
compatibility analysis as for prior data selection
- don't consider the fact that this approach will give different results 
according to the arbitrary depth of the phylogenetic analysis
- charge all molecular analyses of being algorithm-biased, all molecular 
data sets of being "phenetic", never even attempt to make use of molecular 
data, and avoid answering people suggesting you should try at least once in 
your life in order to make up your mind

question: pick out inconsistencies, arbitrariness and bias in Grehan's 
algorithm, compare with effective current practice of cladistic molecular 
analyses, and total evidence approaches (be it simultaneous analysis of 
morphology and molecules in one data matrix of separate analyses with 
evaluation of respective contributions)

>It is evident that we are not going to find agreement on some issues and 
>this kind of disagreement is normal to science.

Of course not, it's never evident that scientists can't come to an 
agreement, to the contrary they are expected to try hard and achieve this 
through open rational debate implementing basic rules of logics
hence my invitation to check for logical inconsistencies, arbitrariness and 
bias, all matters of rational debate when we want to compare scientific 
approaches... scientifically

>But if one finds the lack of concordance to be frustrating then please do 
>not bother to comment.

Logics don't take frustration as a valid argument
All your attempts to turn the rational debate in terms of personal opinion 
are scientifically invalid rhetoric, and refusing logics (like refusing to 
use relevant evidence, cf. Fitzhugh) is flatly anti-scientific

Pierre


Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 63
Télécopie : 02 99 61 81 88