Re: Underlying basis of classification (Was: Re Dinobirds)

[Philidor11@aol.com]

Somehow when the url in the hyperlink reached you a period (.) had 
disappeared.  The diverting site I recommended was www.hamsterdance.com  It 
was still active yesterday; hope you enjoy it.
Seems that there are just a few points of clarification to make sure I 
understood correctly:

<<More generally, a hypothesis is a proposition whose truth or falsehood is 
not initially known. (I got that definition from John Merck - not sure where 
he got it.)>>  
Well, I was under the impression that a hypothesis was an assertion of truth 
subject to falsification.  Given that it's not actually true until proven, I 
suppose this comes to the same thing.

<<This is why we usually call trees "recovered results" or "estimates" rather 
than hypotheses - and it's also why so much time and paper are being spent on 
measures of support and robustness for different kinds of trees.>>
Another possible word, if you want one, is 'plausibility'.  The primary 
meaning of the noun seems to fit.  

I said:  <<Unless someone has insisted on the existence of avialae, new 
analysis has produced characters which apparently were present before the 
prior, feather-based analysis and which come to the same result.  This is 
important because it implies that there is not much difference among the best 
results of the cladistic analyses.>>
You said: <<I'm not sure what you mean here.>>
I've never seen the output of a cladistic analysis computer program.  I was 
dealing with the issue of whether the results I do see are significantly 
better than rejected hypotheses (those not used).  Though I had to draw my 
conclusion with analyses that produced the same results (avialae, 
ornithiscians), these alternate sets of characters which both had acceptable 
results told me that a cladistic analysis could also produce contradictory 
results which were both acceptable as far as the program is concerned.  That 
in turn meant that the program is not capable of saying that as far as it is 
concerned there is only one possible good answer for any given animal or set 
of animals.  Or I guess I could have just asked.

<<We don't normally "look at all possible common ancestors."  Rather, we look 
at all possible hierarchies of relationship - or more accurately still, we 
let our computer algorithms do it for us.  That ancestors "exist" on the 
nodes is understood, but
the search is for the hierarchy.>>
I was struggling with the fact that the ancestor would not 'exist' without 
the diagnostic character set, but supposedly the characters did not define 
the ancestor.  This really is an apparent contradiction.  The program gets 
around this problem by creating ancestors and diagnostic character sets at 
the same time and then accepts or rejects based on its algorithms.  In terms 
of what you're saying, the ancestor is implicit in the hierarchies of 
relationship; if there is a node there must be an ancestor.  You'd produce 
the same result by saying there is a set of all possible ancestors, an 
ancestor for animals in every combination; the program just eliminates the 
implausible ones.

<<Morphology and molecules should support very similar trees, and most of the 
time, they do.  Stratigraphy and biogeography should likewise preserve 
phylogenetic signals, and having a tree match stratigraphy (or come close to 
doing so) is regarded as a kind of congruence.  But having biotic 
(morphology, molecules) and nonbiotic
data disagree is not (or should not) be viewed as strong evidence against the 
tree, as the nonbiotic data are not preserving phylogenetic signals alone, 
and we don't know how strong the phylogenetic component is relative to 
others.>>
What bothers me about this is say that a cladistic 'hypothesis' is 
contradicted by subsequent data, finding the 'black swan' in terms of my 
Popper-Tart thread discussion with Mr. Holtz.  There seem to be good reasons 
for saying that the contradictory data should not be decisive.  Are there any 
firm rules for saying that the amount of evidence against a 'hypothesis' is 
sufficient to reject the 'hypothesis'?  Or can you keep on finding black 
swans for a long time without rejecting the hypothesis 'all swans are white'?

You said:  <<We can make hypotheses of ancestral status on the basis of 
negative evidence - "Fossil A does not occur above fossil B, and does not 
have autapomorphies, and is the sister taxon to fossil B, so fossil A might 
be the ancestor of fossil B."  We could always later discover fossil B below 
fossil A, or autapomorphies in fossil A, that would falsify our hypothesis.>>
I said:  <>
You said:  <<Actually, I wasn't oversimplifying at all.  Ancestors should 
precede
descendents.>>     
I was only referring to my impression that sometimes an ancestor continues to 
exist at the same time as and even after its descendants, so it is not 
impossible to find the ancestor's fossils above, with, and below the 
descendant's fossils.  Sorry to be confusing.

<<The key to testing hypotheses is having repeatable observations.  In the 
experimental world, we generate these by replicating the process in the 
laboratory.  But we historical scientists can't do that, since the 
"experiment" has already been run.  Where philosophers sometimes trip is with 
the concept of "repeatable" - it's not the *process* that must be repeated, 
but the *observation* - and as long as we continue to resample from nature, 
we can repeat our observations.>>
Well, as noted in the arbitrary paleontology thread, when cold fusion and 
sheep cloning were being examined, other scientists did not look at the lab 
notes or even the sheep; they tried to follow the recipe from scratch. The 
'resample' you're talking about does allow checking the process with new 
material, though this is still different from the experimental world's use of 
repetition, and I don't think you mean re-doing the same thing the initial 
investigator did on the same material.

<>
While waiting for the new material which might falsify the 'hypotheses', and 
would constitute proof by avoiding disproof (the prediction/experiment test), 
I like the labeling of the 'hypotheses' as recovered results or estimates (or 
even plausibilities).  The only question is the concern about accepting 
falsification, as mentioned above.

Thanks very much!  The inquiry into the nature of a cladistic hypothesis 
really has clarified my confusion about the use of the term 'hypothesis'.