[Taxacom] Molecules vs Morphology‏

[Jason Mate]

I will keep to the boring topic and let others have fun:

> Molecular data
> > > might support an accepted relationship between some taxa, but not for
> > > other taxa in the group being analyzed. The molecular data is supposed
> > > to be infallible for the accepted grouping and yet returns a false
> > > relationship for other taxa. This has occurred in some primate studies.
> > 
> > Accepted
> > how? Supported by what? 
> 
> In primate studies there have been studies that emphasize results that support an 'accepted' relationship such as human, pan, then gorilla, but the same data source produces relationships for other groups that are not accepted (for example putting lesser apes closer to humans and African apes than orangutans).


My bad, my question wasn´t clear enough: what is your logical basis for deciding that one result is false versus another one? Furthermore, don´t you think that the term, false, implies knowledge of historical truth that, by definition, is probably unknowable? And in regards to your example, do you mean to say that they stress the results that are congruent with others but simply mention in passing other novel ones? Duh!, the first set has external support (congruence) while the latter doesn´t but they´ll mention it just in case somebody else gets similar results.

> No, I am accepting the fact that several researchers
> > using different lines of enquiry and data have reached the same
> > conclusion! That is the hypothetico-deductive model which I have to
> > insist asking again, are you using it or do you use a different one?
> 
> When here is congruence no one has a problem with the results.
> 
> >No data source is infallible in any group or at all levels. 

> Agree 10%

What about the other 90%. 

> When the first molecular
> > phylogenies came out some where so different that one had to wonder
> > what they were sequencing. It is logical that you expect a degree of
> > congruence or otherwise you cannot append your new data. But why is the
> > phenotype the absolute gold standard to which everything should measure
> > to exactly? Please explain in more than one sentence.
> 
> I cannot for the simple reason that I do not view the phenotype this way. If your read the recent publication on the orangutan theory you will see that our principle argument is that the morphological evidence is not necessarily falsified by the molecular incongruence. I can not offer a recipe for anyone to make a decision about that. For me, I find the fossil correlation intriguing to say the least. But for others it may be irrelevant.

No, no, no, don´t look into (o through) the Orangutan´s eyes! If your results are not falsified by molecular datasets is the reverse also true? Because if it is then there is nothing to compare. And the fossil correlation? To what? I honestly do not follow the trials and tribulations of anthropology and its favourite topic so you have to tell me how this specific example is the crux of molecular vs morphological argument.
 
>> Regarding Homo, Pan & Co. (sigh) IF there is incongruence between one
>> dataset and another, this conflict is, of course, in need of more data.
 
>Or different concepts or different perspectives on the data. More data does not necessarily provide a solution. 
>If they dig up a hominid that is a clear precursor to the currently known bipedal morphologies, and this hominid 
>looks even more like an orangutan than current hominids, I might say this additional data adds further support 
>to the orangutan evidence, whereas molecular systematists might say that it is irrelevant in some way.
 
John, that is not true, and we both know it. Everybody loves a good old "missing link" to settle debates. Not to mention 
that such fossil is just novel data and as such supports my position: if in doubt get more data.

>> That said I go back to my second line. If the average of hundreds of genes
>> (or whole genomes as Kenneth pointed out) gives one result that conflicts
>> with morphology then you have to argue that the weight (sheer volume) of
>> data should be the trump card.
 
>Yes - if one is a pheneticist and rely on overall similarity through the law of large numbers. 
>If the law of large numbers is applied to morphology one will get a human-African ape relationship every time, 
>just as one might get a crocodile-lizard grouping every time. 

Sigh, not fair to use the "molecular data is phenetics" card when pressed into a corner. Because then your argument 
falls into a data quality issue which as I have been trying, unssuccessfully it seems, to point out, is a moot point as 
the distinction is not there. A large number of characters is a large number of characters. Mind you, I don´t mean that a 
sequence that is 1000bp long with 100bp which are variable and "informative" is better than 50 morphological characters.
Obviously a single point mutation cannot have the same weight as a morphological character (OK, some of the morphological 
characters out there are probably as weak but lets simplify the argument). However, if I have 50 genes, both nuclear and
mitochondrial, and they point one way, and the morphological data is in conflict... lets just say the morphological dataset 
needs some explaining.


Best

Jason

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