[Taxacom] Molecular phylogenetic hypotheses

[Steve Manning]

At 10:45 PM 8/17/2010, Stephen Thorpe wrote:
> >But your argument from 'different kinds of evidence' means nothing to me. I
> >could just as well parse all observations as 'different'

I think conjunction of evidence IS better than its components, not 
because the majority is always right, but because it more often 
is.  Probabilities should always be considered, much as it is in 
parsimony analysis, be it morphological or molecular or something else.

Steve

> >
>
>Maybe the "different kinds" thing was a red herring. The main point is this:
>As a general principle, I don't see why a conjunction of evidence is 
>any better
>than any of its components. It might be if they all agree, for then 
>you may have
>independent confirmation. But if they disagree, then I don't see 
>what advantage
>is to be had by combining them??? Is the majority always right? You 
>has better
>use lots and lots of components, or else if the results of each are 
>random, you
>could get a majority consensus purely by chance ...
>
>
>
>
>________________________________
>From: Kirk Fitzhugh <kfitzhug 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 3:20:36 PM
>Subject: RE: [Taxacom] Molecular phylogenetic hypotheses
>
>
>Well, ok. But your argument from 'different kinds of evidence' means 
>nothing to
>me. I could just as well parse all observations as 'different' and 
>thus claim it
>useful to infer individual cladograms for each separate character.
>
>Your example works on the presumption that one 'knows' the explanation of
>observations prior to inferring the explanation. This does nothing 
>to forestall
>the total evidence requirement. Again, it's the matter of evidential 
>relevance.
>And it is that relevance that one uses to decide what comprises the evidence
>that goes into an inference.
>
>
>-----Original Message-----
>From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
>Sent: Tue 8/17/2010 6:47 PM
>To: Kirk Fitzhugh
>Cc: TAXACOM
>Subject: Re: [Taxacom] Molecular phylogenetic hypotheses
>
> >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??
> >
> >
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