Re: Feathers are not magical things...

["philidor11" <philidor11@snet.net>]

<Searching for "parsimony" on the dinosaur list archives yeilds 403 matches.
Many of these will link you into previous discussions on this list,
involving many current and past list members.>

Many involve me.  One reason for the discussion to clarify things for me is
a difference in approach to argument.  You tend to state principles, then
add modifiers.  I tend to try to combine principle and modifiers into a
single,
comprehensive statement.  Assembling all that you say, following your way of
explaining, my questions do get resolved.

For example, in reponse to my assertion that:
<So, anyone with a character list and PAUP would not necessarily be able to
produce a 'scientific' cladogram.>
you said:
<However, anyone who knows the principles of the discipline can produce a
scientific cladogram: if you think that I am saying only some "qualified
Ph.D.s" should due this, you are VERY VERY far from the truth!!!>
but then in commenting on my observation:
<There are certain conclusions which can be dealt with by simplicity, such
as the examples that you gave, but producing a hypothesis about a whole set
of relationships involves application of a range of other knowledge.>
you stated:
<True, but within each of those other disciplines, simplicity/parsimony is a
major criterion for choosing between alternatives.>
You also said:
<Certainly if you had a set of alternative equally
well-supported (on morpho or other tree-generating data) phylogenetic
hypotheses, and only one of these was well-supported by an
independantly-well-supported paleogeographic model, then this might help you
prefer that one tree.  Reciprocal illumination is common in lots of
sciences.>

So, if someone like me, say, were to produce a cladogram, using the software
correctly and making my own choices about how many and which characters
(given my definitions) and species to include, you would be able to evaluate
that cladogram using information I don't have.  I think you'd be far more
likely to be able to send my cladogram back to the drawing board than I
would yours.
Can I produce a 'scientific' (using your split between software and
evaluation) cladogram?  Yes.  I'm not disagreeing with you.  Should it be
evaluated solely on the basis of whether I used the software correctly?  No.
I was putting both pieces, creating the hypothesis and evaluating it with
additional knowledge, into the definition of a 'scientific' cladogram.
You're saying that the evaluation portion is not necessary to regarding the
hypothesis as 'scientific'.
If this is correct, then I think I get it.

Accepting this, my statements about the hallmarks of a 'scientific'
cladistic hypothesis should be considered as about the implicit assumptions
both built into the
software and also used by the person interpreting the results.

In response to my formulation that:
<So, a scientific argument about relationships includes:
- a number of shared characters judged sufficient to indicate that certain
animals are related and few enough shared characters in animals outside the
group that these animals can be excluded,>
you responded:
<Not exactly.  It is the concordance (or consilience, or whatever similar
term you'd like) of the characters, not the number.  Certainly a higher
number of uniquely shared characters helps, but is not necessary (nor, in
fact, sufficient).>
Sorry, I don't understand this.  I've seen many summaries here which claim
to prove relationship by a long list of shared characters, with no further
analysis of why the characters are shared.
Is there something in the character selection which is essential to
validating the conclusion?  Thinking of the words consistency and
confluence, you seem to be implying that there must be some connection among
the characters selected before they can be used.  If this is true, then what
I was calling the evaluation component of the development of a 'scientific'
cladistic hypothesis actually would be included prior to using the software.

This same difficulty with a priori/a posteriori arises in understanding your
statement that:
<(Something distresses me in your above point: it sounds to me that you are
confusing phenetics (which clusters taxa based on some metrics of
similarities) with cladistics (which clusters based on the simplest
distribution of derived character states)).>
I'd assumed that cladistics brings together animals based on similarities,
then creates a time line (basal/derived) based on differences.  In
descriptions of the use of software I've seen, there is a prescreening of
which animals to include.  That prescreening and the later grouping into
lineages (with 'sister' groups distinguished) both sound like your
description of phenetics.  These two concepts seem to be conflated.
How are they distinguished?

My second hallmark of a scientific argument about relationships was:
< - expectation that unknown characters will be consistent with others in
the group, as in feathered velociraptors,>
and you responded:
<Yes. I also assume, without additional direct evidence to correct me, that
all dinosaur species had eyes...>
Ok, I'm learning.
Still, what made Jura's assertion (that to be 'scientific'ally valid a
character had to be observed) interesting to me was the fact that the
'scientific' method starts with observations and attempts to find a
principle uniting these observations.  You're extending the use of the term
'scientific' not just into the hypothesis, but into the inferences drawn
from the hypothesis.  There is not only a 'scientific' method; there are
also 'scientific' inferences.  (I had thought the implications of a
hypothesis were to be used as predictions to test the hypothesis, and not as
'true' statements in themselves.)
This usage means that the same term can be applied to things you know are
true because you've seen them and ideas derived logically which do not have
the same degree of confirmation as a Theory, such as tectonics, Evolution,
or Relativity, and also to the concomitants of the hypothesis.
The problem for me is that when you apply 'scientific' to unconfirmed
concepts, it seems you're encouraging the view that science does not
discover Truth (describe reality), but only generates useful, refutable
ideas.  As pointed out in the Disparaging Popper discussion, this could turn
science into a social event.  That is, the ideas considered and in use may
be in part the result of the preconceptions of the people holding them.
Einstein replaced Newton because Relativity was closer to actuality, it
successfully explained/predicted more, and not because we choose to think of
the world in a different way.  You know that; I may be overly sensitive to
connotation, but the extension of the term 'scientific' to the implications
of an unconfirmed hypothesis just seems iffy.

My third hallmark of a scientific argument about relationships was:
<- expectation that evolutionary change in the group will be gradual and
consistent (after all, if a large number of brand new characters suddenly
appeared in the lineage,  the character similarity screen might fail to
identify the
animals as part of the group),>
To which you responded with principle:
<NO!  This assumption does not exist within phylogenetic methodology (or at
least morphological phylogenetic methodology).  The acquisition of large
amounts of new characters within a lineage are not a problem per se: they
will only add a long branch length to that particular (apomorphic) clade.>
and modifier:
<That being said, large scale transformations which "overwrite" a large
portion of the anatomy may obscure ancestral relationships, which is one
reason for trying to find new fossil taxa.>
So, if I'm reading you correctly, my statement would be correct if and only
if I make the assumption that our knowledge of the fossil record of a
particular set of animals is so incomplete that we (or, better, you) could
be misled by a major change in anatomy.
You're right; I did make the assumption that the fossil record should
invariably be considered incomplete.  How do you know that the record on a
particular set of animals is complete enough that this assumption does not
apply?

Finally, in relation to my last hallmark:
<and
- survival of the logically determined hypothesis after application of other
theoretical constructs, including models of adaptation and functional
morphology, patterns of biogeography and the other examples given above.>
I asked:
<Suppose you could establish that PAUP gave a lower weight to punctuated
equilibrium scenarios than to more gradualist models.  Would that invalidate
the algorithm?  I realize that this must have occurred to other people; I'm
asking because I can't solve it myself.>
and you replied:
<Interesting thought.  In the particular case in question, I think the whole
situation is flip-flopped.  I think the failure of resolution of the PE vs
PG question (which dominated a LOT of my classes as an undergraduate and
graduate, far more so than systematics) is that to effectively test models
of these two questions you need well-supported phylogenetic trees.  Even
better, to test some of the particular models you would need to account for
*all* the taxa within these trees.  Unfortunately, relatively few clades of
fossil invertebrates have been subjected to explicit phylogenetic analysis
at present, although some groups are getting addressed.  Within ten to
twenty years, I expect that enough of the relevant speciose and
individually-abundant taxa will be sorted out so that we can go back and
address many of the questions raised by Eldredge and Gould and Stanley and
company.  (Okay, some sooner than others).>
The first question that comes to mind is how reliable the current
phylogenetic trees should be considered while waiting for these
investigations and analyses to be conducted.  I get the impression that the
software as currently constituted may be more amenable to use with one model
rather than another, though I may well be inferring too much.
I also note the use of invertebrate results as a check on vertebrate
analyses.  Is there a way of confirming the appropriateness of this
assumption?  Do changes in snail shells over time parallel changes in bone?

Thanks for so much attention to this discussion!  Dealing with implicit
assumptions rather than direct explication of ideas seems to require a long
windup before the pitch can be thrown.  Hope I haven't balked too often.








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