3TA (correction)

Ren� Zarag�eta i Bagils rzb at MNHN.FR
Fri Apr 11 20:10:50 CDT 2003

(Sorry to P. Hovenkamp for double post, I replied to him, not to the list)

Peter  Hovenkamp wrote:
"Off-list David informed me that I had, indeed, made a beginner's mistake.
Oops. Sorry.
I had mistaken the resolution of the basal node for a real supported
resolution. In fact, it is only supported by the decision to use an
outgroup - which defines the in-group.

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.

Peter Hovenkamp"

In fact, 3TA-proponents also prefer parsimony. Parsimony is used to find the
shortest tree to explain 'data'. The difference between what you call
'parsimony' and 3TA is how to describe 'data'.
3TA was first proposed as "a more precise use of parsimony" (Nelson, G. &
Platnick, N. I. 1991 Three-taxon statements: a more precise use of
parsimony? Cladistics 7: 351-366)
So it should be more precise to replace 'parsimony with 'standard parsimony'
in your post. "Standard parsimony" is an algorithmic implementation of
parsimony criticized by 3TA proponents.
I don't understand your reference to intuition (unless you think 3TA is
intuitive, which i don't).

P. Hovenkamp's answer to my post:
>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".

There are lots of other cases, independently of probabilities, and I don't
call it "taxonomic judgement", but parsimony.
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.
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
optimization). 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.

René Zaragüeta

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