[Taxacom] Molecular phylogenetic hypotheses

[Stephen Thorpe]

yes, I was simplifying it a bit for brevity, but substitute "rational basis for 
belief" for "truth" and the question still stands:

does a more complete set of data give you any more rational basis for belief in 
a conclusion? Think of it this way: a subset of data (say morphological) points 
to a conclusion which you don't accept if it contradicts that of another subset 
(say molecular), but does adding more data necessarily help? Suppose we have 
"complete data" and it points to a particular conclusion. Why is that conclusion 
any more rational to believe than any contradictory subset? The BIG assumption 
here seems to be that subsets point to the wrong conclusions simply because they 
are only subsets (i.e., incomplete), and any conclusion that the complete data 
points to is to be preferred on the grounds that it is complete data. But 
perhaps both incomplete and complete datasets can point to the wrong conclusions 
for any number of reasons unconnected to completeness??


________________________________
From: J. Kirk Fitzhugh <kfitzhugh at nhm.org>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Cc: Bob Mesibov <mesibov at southcom.com.au>; TAXACOM <taxacom at mailman.nhm.ku.edu>
Sent: Wed, 18 August, 2010 12:24:42 PM
Subject: Re: [Taxacom] Molecular phylogenetic hypotheses

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
>
>_______________________________________________
>
>Taxacom Mailing List
>Taxacom at mailman.nhm.ku.edu
>http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>The Taxacom archive going back to 1992 may be searched with either of these 
>methods:
>
>(1) http://taxacom.markmail.org
>
>Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  
>your search terms here
>