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Re: REPLY TO WAGNER'S POST: 21 AUGUST 1997 CONCERNING CLADISTIC SHORTHAND [long, but not about sickle claws...]



        -->From now on, it would probably be best if we continued this
discussion off list. Anyone with comments, please send them to
Tetanurae@aol.com and wagner@ttu.edu .

At 04:57 PM 8/30/97 -0400, Pete wrote (<<>> quotes me):

>True, I have no argument with your use of any shorthand, except the explicit
>definitions of node and stem based taxa. 
        Huh?

>It is my position that your shorthand is too long, and overly complicated.  
        Indeed, I would say that yours is overly complicated (too many
symbols, too dependant on sequential ordering). As for too long:
        {A > B} Is one character width shorter than my method's...
        {+A, -B}

>NODE BASED
><<I believe that putting th +/- in front of the anchor taxon name
>makes the definition *visually distinct*, and highlights the unique role of
>the anchor taxon in the definition. It is unlikely that a taxon definition,
>so denoted, will be confused with any of the above shorthands. For example:>>
>
>This is indeed correct, but it is also unnecisarily complex.
        Deliberately so. This is done on the one hand to distinguish from
the other types of cladistic shorthand, on the other hand to highlight the
importance of anchor taxa to the definition, and on the gripping hand to
make you *think* about how you are defining (or using) a phylogenetic taxon.

>I believe you
>express some concern that if a node based taxa is defined verbally as "the
>most recent common ancestor of both A and B, and all of its descendants", it
>is somehow dissimilar to {A + B}.
        As I meant to illustrate in my review of shorthand uses, "{A + B}"
Can potentially have several meanings. All tend to describe a clade, but it
is difference between *description* and *definition* which I believe should
be emphasized in any shorthand.

>In other words, you suggest that {A + B} implies an ultra-exclusive
>relationship, which it does not.
        I do not understand your point. All clades are totally exclusive or
animals outside their scope, and totally inclusive of those within. The only
question is what animals are within the scope, and which are not. There can
be no superlative modifiers to this concept.

>It cannot.  In truth, this is simply
>absurd, one cannot ever really know EVERY animal that is included within a
>clade, and to pretend to do so is simply silly.  To imply that shorthand
>definitions do so, is silly as well.
        By definition, a clade *does* include every animal which meets its
description, whether or not the animal is known or not. This is the beauty
of monophyletic groups.

>As to why I favor {A + B} as a opposed to {+A, +B}?  Simple, it has less
>keystrokes, and is thus shorter shorthand, and is just as understandable.
        As demonstrated above, your method uses seven keystrokes, mine uses
eight. You will note that, as taxon names get longer, this difference
diminishes, asymptotically approaches nought. I have attempted to show that
your method is not necessarily just as understandable, and it has great
potential to be confused with shorthands used for other purposes. In that
light, saving one keystroke is hardly worth the trouble.


><<I do not think Pete's use of the | "or" symbol is beneficial. It is
>not clear exactly clear what the "or" means. For example {A > B | C}>>
>
>Why not?  How are stem based clades that include one organism, but exclude
>two or more others defined verbally?  Is it not: "All those organisms that
>share a more recent common ancestor with A, than either B *or* C"?
        This is, IMHO, a shortening of "all animals which share a more
recent common ancestor with A than they do with B, and also share a more
recent common ancestor with A than with C" (as Nick Pharris has pointed out
to me). The statement you quote above is almost as ambiguous as your shorthand.
        "Or" is simply not an explicitly outlined concept in this
definition. Now, bear in mind that this may be corrected simply by
understanding the over meaning of the shorthand. SOme degree of
interpretation will always be required. I find, however, that my method is
less ambiguous.

>To be more clear, I guess you could define it doubly, like: "{A > B} & {A >
>C}", but to me, that is unnecisarily long and confusing.
        And, I will readily agree, unnecessary.

>Again, I prefer my method over Wagner's simply because it has less
>keystrokes, and is a shorter shorthand.
        By one keystroke.

>Then use another symbol.  I use | at the suggestion of Mickey Rowe because he
>said that it kept with the math theme more than commas, slashes, or the word
>'or'.  We could use @ for all I care, just a symbol that we agree means 'or;'
>in the context of cladistic shorthand.
        The proliferation of symbols is to be avoided at all costs. Also,
the more one's shorthand appears to be a mathematical formula, the better.
You will note that my shorthand is isomeric (I think that's the correct
term). There is no order in which anchor taxa must be listed in my shorthand
(although it is recommended that inclusives be named first). It is simply a
quick way of listing the anchor taxa of a higher taxon, and their function.
For example:
        {+A, -B, -C} = {-B, +A, -C} = {-C, -B, +A} etc.
Whereas, in Pete's system:
        {A > B | C} != {B > A | C} != {C > B | A}

Note: I put spaces around the | symbol. Good for the eyes, says I.

><<While I think the use of <> is ingenious, it does not work without
>some sort of "or" symbol,>>
>How doesn't it?  Isn't, say, Neoceratopiaia defined verbally as "All those
>animals that share a more recent common ancestor with _Triceratops_ than with
>_Psittacosaurus_"?  Thus being: {_Triceratops_ > _Psittacosaurus_}.  I don't
>see how this doesn't work....
        Excuse me. This should have read "does not work in instances of
multiple exclusive anchor taxa without an "or" symbol". Sorry. :)

><<and it still does not *explicitely* denote anchor taxa.>>
>How doesn't it?  The single taxon to the left of the '>' is the inclusive
>anchor, and all the others to the right of the '>' are the numerous excluded
>anchor taxa.  It does not imply that the excluded taxa form a clade, just
>that they are excluded.
        Yes, but it it does not seperate their function explicitly as
anchors rather than as included members or OTUs. Look back over the other
forms of cladistic shorthand I listed. In the non-definitive shorthands, the
names of taxa serve a different purpose. They are not being used to *define*
a group, they are simply members of a group, or OTUs in a study. I cannot,
with mis ojos, tell from your shorthand that the anchor taxa serve an
explictly definitive function. I may know this from your text, but {A + B}
looks a lot like {A + B} and (A + B) and A + B, which can all serve
different descriptive functions, and where A and B may be performing any
number of disparate roles.

><<The +/- prefix also emphasizes the differring function of an anchor
>taxon, as not necessarily being included in the group, but fundamental to
>the definition of the group.>>
>Just as the '>' does, but with less redundant keystrokes.
        As I just demonstrated, it does not. Further, as I have just
demonstrated, there are not sufficiently fewer redundant keystrokes to make
a significant difference. Further, while you are making those redundant
keystrokes, maybe you (pl.) might think a bit more about what those
redundant keystrokes mean, and how you are defining the taxon.

>In addition to the squggly brackets, '/' could be used,
>as it is by some linguists to seperate something from the rest of the text,
>ie with the definition of Neoceratopia: /_Triceratops_ > _Psittacosaurus_/.
> I don't like this from a purely asthetic point of view.
        Agreed.

>Additionally, '<' and '>' could be used, but these would be confusing as
they >are already used within the definition of stem-based taxa.
        Only in your system. They are, however, potentially confusing,
aestheticaly displeasing, and do not seem to be a part of the general
qausi-mathematical character set in this context.

><<Hopefully, we'll all reach some sort of happy, useful middle ground
>at some point.>>
>Indeed.
        But not before we duke it out over a beer. Chicago?

        :}
        Wagner
----------------------------------------------------------------------------
    Jonathan R. Wagner, Dept. of Geosciences, TTU, Lubbock, TX 79409-1053
               "Not the One..." -- Zathras (not Zathras)