3TA (correction)

P.Hovenkamp Hovenkamp at NHN.LEIDENUNIV.NL
Mon Apr 14 10:47:09 CDT 2003

At 08:10 PM 4/11/03 +0200, René Zaragüeta i Bagils wrote:

(What went before...)
I wrote:
>When analyzed properly with an outgroup, Davids example indeed holds:
>parsimony does not reconstruct a group (BCD). Using parsimony, there is no
>character support for this group. That raises an interesting point: what
>makes the presence of this group so glaringly obvious to most people
>looking at this matrix:
>O 00
>A 00
>B 01
>C 10
>D 11
>Intuitively, we appear to argue that B and C are both closer to D than A is
>to D, so they must be in the same cluster. Is our intuition wrong, or is
>cladistic parsimony all wrong?
>David (and the other 3TA-proponents - this matrix is a derivation of an
>example given by Nelson in his "Nullius in Verba" paper - sorry, I don't
>have the reference) seem to prefer intuition. Others prefer parsimony, on
>grounds that have been debated extensively.

Rene wrote:
>I don't understand your reference to intuition (unless you think 3TA is
>intuitive, which i don't).

And I answered:
> >The main argument in favour of 3TA seems to be that this matrix when
> >analyzed with standard parsimony (OK, I'll accept this correction) does not
> >give the solution (BCD). I have seen no arguments why it should give that,
> >except that it seems obvious. I call that intuition, but you may prefer to
> >call it "taxonomic judgment".

Rene again (and I intend this to be my last contribution to discussion 
until Rene can come up with an argument that is not based on a 
misunderstanding of common concepts (see also Kirk FitzHugh's post):
>There are lots of other cases, independently of probabilities, and I don't
>call it "taxonomic judgement", but parsimony.
Apart from what we call it, the question was - why do you prefer the 
outcome (BCD) over the outcome (ABCD). No answer.

>Standard parsimony proponents place themselves always from the "I have the
>true solution" viewpoint, so any potential refutation is seen as bizarre,
>rare, intuitive or understandable in terms of probabilities, etc.
This is almost complete gibberish. Refutation of a statement occurs when a 
new observation is made that contradicts this statement. The only "new" 
observation that has been presented so far is:
"sometimes, standard parsimony gives results that are not the same as the 
results of other methods"
And that observation is hardly new. In fact, standard parsimony was 
developed as an alternative to a number of these other methods, which would 
not have been necessary if it would always give the same results... And 
what statement could it possibly refute?

>But the point is not that this matrix is something in favour of 3TA.
>Corroboration does not mean anything (see R. Jensen's post about Jaccard's
I've seen it. It is interesting, in that it points out that what I called 
the intuitive solution, and what 3TA proponents obviously see as the best 
solution for the problem, can be obtained using a particular phenetic 
coefficient.  It is not about corroboration. Corroboration is one of the 
possible outcomes of a attempt at refutation. About which see above.

>The point is that this example is a potential refutation of
>standard parsimony. You have to answer in terms of standard parsimony, not
>in justifications against 3TA.
The example is simply one in which a particular phenetic analysis results 
in another outcome than an analysis using standard parsimony. It does not 
refute anything at all.

Peter Hovenkamp

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