[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Subject Index][Author Index]


I am finally getting around to replying to this post by Jon Wagner on
cladistic shorthand.  If cladistics either does not interest you, or bores
you to tears, read no further.  If it does interest you, then please continue

<<Peter B. wrote:
>*Again in this post, I have used my own brand of cladistic short-hand
>which differs from Jon Wagners.
        But not by much...>>

True, I have no argument with your use of any shorthand, except the explicit
definitions of node and stem based taxa.  It is my position that your
shorthand is too long, and overly complicated.  I'll explain why below.

<<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.  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}.

In other words, you suggest that {A + B} implies an ultra-exclusive
relationship, which it does not.  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.

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.

<<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"?  If it
isn't, correct me, but that is how I understand it.  Thus, the shorthand
'phrase' {A > B | C} is simply stating the verbal definition.  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.

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

<<If I have an animal [organism X  --P.B.] more closely related to A than it
is to C, but
more closely related to B than to A, is it still part of the group? In other
words, should I read this as "all animals more closely related to A than B
or to A than C"?>>

No, of course not.  The topology would be:

(C, ((B, X), A))

Thus, organism X would form a clade with B, which is already explicitly
excluded from the stem-based group anchored by A, so X is excluded as well.
<<Also, it should be noted that in probability the | means "given". So
the statement above would read: "All animals more closely related to A than
B, given C.">>

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.

<<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....

<<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.

<<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.

<<My system uses curly brackets to surround the definition. These were
intended to emphasize the distinctness of definition versus description.
Using them in case number 2 above makes this less effective, but it is still
useful. Peter likes this idea too, so maybe it has some merit...>>

Yes, parenthesis simply get confused with parenthetical notation, or
citations, or prenthetical explanations.  Square brackets get confused with
editorial comments.  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.  Additionally, '<'
and '>' could be used, but these would be confusing as they are already used
within the definition of stem-based taxa.  So, yes, squiggly brackets it is.

<<Hopefully, we'll all reach some sort of happy, useful middle ground
at some point.>>


Peter Buchholz

Los Angeles loves love.