[Taxacom] Molecular phylogenetic hypotheses

Tue Aug 17 20:47:11 CDT 2010

>Conclusion A is more rational than B if it is the case that A was inferred from 
>one's total available relevant evidence and B was only inferred from a subset of 
>that evidence

this I don't buy, at least not in cases like the present context where there are 
radically different kinds of evidence (morphological, molecular, ...) Suppose, 
for example, that convergence was the cause of great morphological similarity, 
but the genes alone give conclusion A. Suppose, for the sake of argument, that A 
is the true/best/... conclusion, but the convergence is such that the 
morphological similarities outweigh the genetic/molecular data, so total 
evidence doesn't allow you to infer A. How can it be more rational to use bad 
evidence? Of course we don't typically know if some evidence is bad, and therein 
lies the problem ... we don't typically know which evidence to exclude ...

________________________________
From: J. Kirk Fitzhugh <kfitzhugh at nhm.org>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
Sent: Wed, 18 August, 2010 1:21:52 PM
Subject: Re: [Taxacom] Molecular phylogenetic hypotheses

It's not a matter of 'more complete' versus something lesser. It's a matter of 
the relations between the basis for inferring some hypothesis given some set of 
evidence. In the event there is relevant evidence that's being actively 
partitioned out of an inference, then there is less of a rational basis for 
accepting that conclusion/hypothesis. Worse yet, actively comparing branching 
diagrams is a meaningless exercise - the two diagrams don't matter to one 
another, since each only applies to the premises/evidence used in the inference.

Re "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?" What's the empirical 
basis for accepting the conclusion beyond the premises used to make the 
inference? The conclusion can't 'contradict' a conclusion derived from some 
other class of observations. The two conclusions are irrelevant to one another. 
Don't confuse a simple branching diagram with an explanatory hypothesis.

"Why is that conclusion any more rational to believe than any contradictory 
subset?" Rationality is a relation between premises and conclusion. Conclusion A 
is more rational than B if it is the case that A was inferred from one's total 
available relevant evidence and B was only inferred from a subset of that 
evidence.

"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??"

Just like 'truth' throwing around 'right' and 'wrong' is just not appropriate to 
this issue. We're only talking about going from observed effects to a hypothesis 
that offers an impossibly vague explanation in the form of a cladogram. To speak 
of whether or not some hypothesis is 'right' or 'wrong' only matters at the 
point one goes out and actually follows the established mechanics of putting 
that hypothesis to the test.

On 8/17/2010 6:00 PM, Stephen Thorpe wrote: 
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
>>
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