[Taxacom] Morphology vs Molecular

[Scott Fisher]

Please honor the following promise:

"I have had a good number of years of interesting discussions, but legal threats are not something I want to contend with. This is my last posting.

John Grehan"

Thank you,

SF



________________________________
From: John Grehan <jgrehan at sciencebuff.org>
To: Taxacom <taxacom at mailman.nhm.ku.edu>
Sent: Monday, August 17, 2009 11:46:24 PM
Subject: Re: [Taxacom] Morphology vs Molecular



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
Sent: Monday, August 17, 2009 8:09 PM
To: Taxacom
Subject: [Taxacom] Morphology vs Molecular


>Obviously my results contradict molecular results.
> Huh? So molecular studies do not contradict yours but yours contradict 
> theirs? Please explain.

They each contradict each other. Ok?

> The definition is a posteriori. If the reanalysis including the extra 
> information renders your previously homologous character states 
> homoplasious, is this the wrong kind of information?

No, it's the right kind of information in that the features were uniquely shared within the ingroup, but did not conform to the best supported arrangement of inferred relationships.

> Ah yes, ye old know thou homology. The problem is that just because two 
> structures are homologous the change might not be (i.e. enamel in teeth 
> might thin in Orangutan´s because of soft fruit diet but in humans, 
> separately, because of food processing). 

Its actually thick. It is not only homology, but uniquely shared features.


> Even molecular datasets compare homologues (although there are cases where 
> paralogues have been compared by accident; same with non homologous 
> morphological strctures).

But they assume derived conditions (when they consider that at all, because they have no trace of what base replaced what base). Similarity is all that there is.

> Your definition is just a throwback to preHenningian phylogenetics where 
> "only relevant characters"
> are used (the definition being that of the author). The final analysis is 
> just a mere formality.

True, cladistics does predate Henning. But the definition is clear, if a feature is uniquely shared within the ingroup then it is a potential synapomorphy. The largest set of congruent features indicates the most probable phylogeny.

>Right. That is my point, it could be either way. The assumption has 
>been that the morphological
> results need 'explaining' as if the incongruent molecular results do not.

Please John don´t put words in my mouth. 

> Don't think I did. It was what you appeared to be saying.

> The only objective way to decide which phylogeny best represents the truth
>  (by definition unknowable) is congruence, congruence not only to one 
> dataset but as many as possible.

I would agree if the data are of the same kind.

> Phylogenetics is based on data objectivity (i.e. treating all data as 
> equal) and "parsimony" (greatest explanatory power). 

Agreed - if the data are all derived states.

> Your counterargument is to say that molecular data is phenetic (how you got here is anybody´s guess) 

No it is not just a guess. We outline the argument in our paper.

> and that a unique and intimate knowledge of the characters (read, I have 
> been doing this for years so trust me) trumps any amount of contradictory
>  data (information that it not of the right kind).

That remains to be seen

>Unfortunately, working 'for' molecules and morphology is not so
straightforward. Of course morphological inheritance has a molecular counterpart, but this does not automatically mean that current methods of counting base similarities is necessarily the best way of capturing this or any other phylogenetic signal, or better than morphological evidence. 

> John, do you even realise how deeply biased, to the point of obfuscation,
>  you are? Base counting (the molecular equivalent of reading pig knuckles)
>  versus morphological evidence. The word is data! for both.

Both are data, yes, but one type of data is more problematic in my opinion. But of course that is a minority opinion.

>The law of large numbers is invoked, but its just a
> theoretical or philosophical principle, and one that was used in the past 
> by morphologists who tried to argue that the more similarities included the
>  better the result.

> Yes, expert knowledge (preferably ones own) should be the standard.

Word's in whose mouth?

>The present conundrum facing systematists is how to decide between
> conflicting base counting similarities and morphological similarities.
> If the former is accepted as falsifying the latter then we have a real
>  problem in hominid evolution where the fossil record shows morphological
>  relationships that are congruent with morphological relationships among 
> living taxa. 

> I can live with that. I happen to think that cladistics is more than ones 
> own little plot.

Does that agreement mean that I have made a valid point?

>This would have to be dismissed as phylogenetically
> meaningless if the molecular theory of relationship among living taxa is 
> accepted - and this is what is happening at present, even though the 
> molecular evidence cannot inform the relationships between fossil taxa, or 
> between fossils and living taxa.

So if you accept molecular data then you are ignoring paleontological data?!
John, please stop and think carefully about this line because it is simply an emotional gut reaction seeking support.

It would seem that one would have to ignore the paleontological data that groups fossil hominids with orangutans and not African apes.

Cheers, 

John Grehan

Best

Jason

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