[Taxacom] Molecular phylogenetic hypotheses

[J. Kirk Fitzhugh]

  There are two answers to your query: (1) there is no guarantee any 
inference will give one a true [sic] conclusion (except in deduction); 
(2) the notion of truth is irrelevant to the issue (the matter at hand 
is one of having a rational basis for accepting a particular conclusion 
based on available premises/evidence). Talking about 'truth' only comes 
into the mix when one actually tests hypotheses - something that is 
almost never done with phylogenetic hypotheses.

On 8/17/2010 4:45 PM, Stephen Thorpe wrote:
> this raises something I have been wondering: in general, if different 
> subsets of data point to different results, why would the "total 
> evidence approach" (i.e. the complete set of data, or at least a more 
> complete subset of data) be expected to necessarily point to the 
> "truth"???
>
> ------------------------------------------------------------------------
> *From:* Bob Mesibov <mesibov at southcom.com.au>
> *To:* kfitzhug at nhm.org
> *Cc:* TAXACOM <taxacom at mailman.nhm.ku.edu>
> *Sent:* Wed, 18 August, 2010 11:37:26 AM
> *Subject:* [Taxacom] Molecular phylogenetic hypotheses
>
> Hi, Kirk.
>
> Many thanks for the draft. I'm copying this portion of my reply for 
> Taxacom because there's what might be seen as a counter-example in the 
> recent literature, which Taxacomers might like to read.
>
> You make the point that a typical molecular systematics research 
> stream consists of building a phylogeny from sequence data, publishing 
> it and moving on (to either another group or the same group with more 
> data) to do the same thing again and again, with no attempt to 
> understand the result. This freely available paper
>
> http://rspb.royalsocietypublishing.org/content/early/2010/08/05/rspb.2010.0590.full.pdf+html
>
> does something more. The authors examine the possibility that the 
> disagreements between certain published phylogenies are due in part to 
> *analytical biases*. They apply very simple tests which support this idea.
>
> What is surprising and disappointing to me is that one or more of 
> those tests might have been done earlier by any of the research groups 
> working on arthropod phylogeny. They weren't. For some molecular 
> systematists, the way to get better phylogenies is to use more or 
> longer sequences and more terminals. The hope here is that if you 
> throw more data at the problem, any systematic biases will be swamped 
> by 'signal'. If there are disagreements between research labs, you 
> *suspect* bias but you don't test for it, maybe because your 
> previously published work would be revealed to be... less than useful.
>
> Perhaps for some molecular systematists, the analytical method of 
> choice is an oracle whose pronouncements cannot be questioned, only 
> published. No wonder you see that sterile sequence-analyse-publish 
> repeat. The same oracle-worship is seen in *choice* of inference 
> method. In a post earlier this week, Thomas Simonsen compared 
> neighbour-joining 'phylophenetics' unfavourably with other-inferential 
> 'phylogenetics'. Thomas might be right in the particular case he's 
> considering, but distance-based trees are often very close to maximum 
> likelihood trees for closely related taxa (you might say 'close within 
> the uncertainty of the method'). Should you not do distance-based 
> analyses because of a philosophical distaste for them, even though 
> they give the same result as another method?
>
> [Hoping this doesn't spawn a long thread, off to the field for several 
> days shortly]
>
> Best wishes,
> Bob
> -- 
> Dr Robert Mesibov
> Honorary Research Associate
> Queen Victoria Museum and Art Gallery, and
> School of Zoology, University of Tasmania
> Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
> 03 64371195; 61 3 64371195
> Webpage: http://www.qvmag.tas.gov.au/?articleID=570
>
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