Traits and/or states

[Jason at]

>I my mind, structure X is a character that exists in two states.  When I
>code
>my matrix for all of the organisms in my collection, I have two choices.
>First, treat the mutually exclusive appearances of structure X as one
>character with two states; the cells of one column (or row, depending on
>your
>preferred orientation) are coded 1 or 2, depending on the observed
>appearance;
>second, treat the two mutually exclusive appearances of structure X as two
>separate characters; for one column, I will enter 1 or "not 1", the second
>column will have 2 or "not 2".

My choice is the former method of coding. I don't see the point of coding a
character with 2 mutually exclusive states in two columns since it is
impossible to have a condition of "present" for both states, which
undermines the whole point of breaking down the character to begin with. And
since we are doing a character coding/analysis Q&A, I would like to add a
question of my own: doesn't the latter method of coding result in similar
information retrieval as 3 taxon analysis?

Cheers

Jason
>
>My question is (I know my answer, but I would like to know how others
>respond), what is the difference in these two coding schemes and why would
>one
>be considered more (biologically, philosophically, phylogenetically, etc.)
>correct than the other?
>
>Cheers,
>
>Dick
>
>
>Quoting Gianluca Polgar <polgar at ALFANET.IT>:
>
> > I would like to express some ideas on the character/states concepts.
> >
> > 1) When we speak of phylogenetic inference, we should speak of
>inheritance,
> > i.e. of vertical transmission of genes.
> > This is a first hypothesis.
> > We know that widespread and iterative events of horizontal transmission
> > (i.e. via retrotransposons or transposable elements in eukariotes) lead
>to
> > impressive evolutionary changes. Maybe the same explosive radiation of
> > eukaryotes and their extraordinary evolutionary versatility with respect
>to
> > the prokaryotes, could take place only due to continuous and iterated
> > genetic duplicative mechanisms mediated by transposition or
> > retrotransposition.
> >
> > 2) But even assuming that horizontal transmission could be treated as a
> > background noise at the scale of microevolution, speaking of inheritance
> > when observing a phenotype (i.e. a morphological structure), implies a
> > biunivocal correlation between shared phenotypic similarities and shared
> > genetic traits.
> > This is a second, strong hypothesis.
> > We know that the morphological structure and related function of an
> > organism is the result of the continuous interaction between the
>organism
> > itself and its "environment", during embriogenesis and ontogenesis
> > (reaction norms, ecotypes...). Shared similarities could only show a
> > similar "interactive history" of the organism.
> >
> > 3) But what is a "character" and its "states" from the point of view of
> > inheritance?
> > The only reasonable explanation for these concepts that I find, taking
>into
> > consideration points 1) and 2), is that the "character" is an
>abstraction:
> > it is the hypothetical "type of stable structural plan" which is the
> > ecological and genetic stable interaction that controls the
>differentiation
> > and development of a complex morphological structure through
>generations.
> > (Note that intended so, the "character" is then linked not only to
>genetic
> > flux, but also to the environmental conditions in which this flux have
> > occurred through generations... but let's follow the second hypothesis).
> > Thus the structural genetic plan could be the "high-level construct"...
> >  From this point of view then, states would be the expression of a
> > particular structural plan, or the interaction between particular
>alleles
> > (i.e. genetic variants).
> > (Note that this is an oversimplification: for each allele, SEVERAL
>reaction
> > norms will be possible in different environmental conditions...)
> >
> > But how could we infer that two particular morphological features of two
> > different species (here more problems arise, but we'd like to arrest the
> > analytical
> > haemorrhage...) which apparently share similarities... ARE actually the
> > outcome of a common (in the sense of a recent common ancestry)
>"structural
> > genetic plan"?
> > We may study their anatomy, physiology, autoecology, eco-ethology (which
> > most often we don't), correlate their observed characteristics with
>their
> > observed functions inside and outside of the organism, and deduce their
> > homology, i.e. propose a parsimonious model of their evolution. This is
>how
> > for instance, comparate anatomy seems to work.
> > We thus recognise in that observed, complex, reasoned cluster of
> > morphological details a "structure" and a "function": an identity of its
> > own.
> > (In an ideal condition, we would analyse the genetic control of the
> > expression and differentiation of that particular phenotypic feature,
>and
> > then compare the genetic distance on the basis of targeted markers...)
> > Thus we may describe a "morphological trait", assuming that its
> > characteristics correspond to an inheritable "structural plan", and we
>may
> > call it a "character".
> >
> > This is a third, very strong hypothesis.
> >
> > Up to this point, seeing that in most cases taxonomists never have the
> > possibility to go through the long and complex experimental and
>theoretical
> > processes needed to support the mentioned hypotheses, isn't it more
>honest
> > and scientifically correct to limit the phylogenetic inference to the
> > subject/predicate constructs directly derived from observations? Nothing
> > more, nothing less of that: a phylogenetic inference based on shared
> > OBSERVED similarities... The subjective (and psychological)
>arbitrariness
> > of this process can be actually limited by a number of considerations,
>and
> > the taxonomist will with no doubt reasonably explain his choice of the
> > characters and of the states... that's all.
> >
> > Best
> >
> > Gianluca Polgar
> > c/o Prof L. Bullini
> > Dip. di Gen. e Biol. Mol. "Charles Darwin"
> > Univ. of Roma La Sapienza
> > Rome Italy
> >
> > >At 10:42 AM 10/31/03 +0100, you wrote:
> > >>The character/state distinction seems to be (to me, at least)
>reasonable
> > >>not only from the purely practical point of view.
> > >>What we call 'character' and 'state' in the phylogenetic analysis are
> > >>indeed both high-level constructs, not observations (not speaking
>about
> > >>all the problems with the process of "observation"). The
>character/state
> > >>distinction is a way how to hierarchize such constructs; we can treat
>this
> > >>hierarchic relation as a subject/predicate, variable/value or whatever
>but
> > >>the language we are using can hardly change the merit. I have
>personally
> > >>found nothing in your message (nor in your presentation referenced
>below)
> > >>what would contradict this generally accepted opinion. Perhaps you
>could
> > >>explain your position in more detail?
> > >
> > >
> > >My thanks to Drs. Skala and Deleporte for their thoughtful comments. I
>will
> > >try to respond here to both.
> > >
> > >I'm not entirely sure I understand what is meant by "high-level
> > >constructs." If descriptions of organisms, or the cells of a data
>matrix,
> > >do not represent our observations, then it would be difficult to claim
>that
> > >a phylogenetic hypothesis is an explanation of shared similarities.
> > >
> > >The concern I have had with the "character" and "state" distinction is
>that
> > >it is not consistent with the nature of observation. What we observe
>are
> > >objects by way of their properties (= character, attribute, trait), and
> > >these are communicated by subject-predicate relations. For instance, I
> > >cannot observe "number of digits." But I can observe that the distal
>ends
> > >of some set of appendages (subject) have five digits (predicate). The
> > >"character," "number of digits," and the "state," "five," cannot
>represent
> > >subject-predicate relations denoting observations since "number of
>digits"
> > >does not represent the subject observed. What are observed are subjects
> > >called appendages with the property (= character, attribute, trait) of
>five
> > >digits. The cell of a data matrix for species X must code the
>observation
> > >that individuals in this class have appendages with five digits. The
>cell
> > >is not simply a "state;" the cell summarizes observations.
> > >
> > >I don't find any hierarchic relation here, and such a relation would
>not be
> > >expected for objects and their properties. On the other hand, an object
>can
> > >be composed of subsidiary objects, in which case hierarchic relations
>can
> > >be stated. But, this hierarchic relation of a part composed of parts is
>not
> > >equivalent to the observations which allow us to speak of the relation
> > itself.
> > >
> > >I hope this helps clarify what I said earlier.
> > >
> > >Best,
> > >
> > >Kirk
> > >
> > >-----------------------------------------------------
> > >J. Kirk Fitzhugh, Ph.D.
> > >Associate Curator of Polychaetes
> > >Invertebrate Zoology Section
> > >Research & Collections Branch
> > >Los Angeles County Museum of Natural History
> > >900 Exposition Blvd
> > >Los Angeles CA 90007
> > >
> > >Phone:   213-763-3233
> > >FAX:     213-746-2999
> > >e-mail:  kfitzhug at nhm.org
> > >http://www.nhm.org/research/annelida/index.html
> > >----------------------------------------------------
> >

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