parsimony/biology

[Thomas DiBenedetto]

-----Original Message-----
From: Kirk Fitzhugh [mailto:kfitzhug at NHM.ORG]
>Curtis Clark wrote:
>>Those individual organisms are not things, they are statements of causal
>>events of ontogeny,

which was in response to Kirk's message which included:
>A "phylogeny," or a cladogram, is a statement of a series of causal
>*events*, not a statement of the existence of a "thing."

Well, just for fun, I will take the third alternative position that seems to
be implied in the context of this discussion (although I sense that Curtis's
point was not so much that organisms arent things, but that they can be
looked upon as events, as can any "pattern" - am I right Curtis?).

Individual organisms are things. A phylogeny, or a cladogram is, most
emphatically, a statement of the existence of things as well. The "things"
that a phylogeny represents are monophyletic taxa. A monophyletic taxon is,
to quote Kirk (who was making a differnt point at the time) "an
individual...(a) non-universal, spatio-temporally constrained entity, i.e.,
a thing".
Kirk argues "...All that are observed are individuals, i.e.,
individual organisms. The patterns one can perceive are the properties
shared among some individuals". I agree. In the process of defining
characters we percieve patterns of shared properties amongst individual
organisms. In a further stage of character definition, we infer that these
shared properties are homologies - they are the "same" things, present as a
result of descent from a common ancestor. In other words we see a pattern
amongst things which we recognize as the various manifestations of a single
historical "thing". And we further propose that this "thing" is distributed
amongst organisms in the way that we find it to be, because the organisms
themselves are "things" that are the varied manifestations of a single
historical "thing" - a common ancestor. This historical "thing", a common
ancestor and all of its descendants - i.e. a monophyletic taxon - is part of
what we are hypothesizing when we code a character and put it in a matrix.
The character thing - hair -found in the organism things - humans,
kangaroos, playtpuses - is in reality the descendant of the original hair
thing in the ancestral organism thing, the ancestral mammal. This group of
hair things form a character homology. This group of organism things form a
monophyletic taxon. They are all things. And these are the things that we
really deal with in a phylogenetic analysis.
Now of course we can then infer from this internested set of things that
there were events that caused the observable diversity of the things. That
is an important and valuable inference that one can make. But events are not
what we observe. We do not construct hypotheses about such events. We infer
the events from the patterns of things that emerges from our observations,
our hypothesizing, and all of the tests that we put those hypotheses
through.
-tom