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Re: =?unknown?b?TPw=?= and Li 2006, a review

David Peters (davidrpeters@earthlink.net) wrote:

<So, Jaime, why make a red herring negatory comment if you are in tacit
agreement with my statement? It makes you look bad, my friend. Argumentative,
just for the sake of being so.>

  Because I did not actually agree with Dave. Yes, it will change the
phylogeny, but not so substantially as Dave implied in his post, which would
argue that the entire phylogeny has to be scrapped because they chose not to
put squamates in the tree. As I stated, one can test the effects of the matrix
solely by inputting their own outgroups. Thus it may shift the base, but the
tree as a whole has suffered relatively little difference. One doesn't really
know unless one tries, however. Not so much argumentative as challenging. As
David Marjanovic stated, it would be much better if one accurately coded
synapomorphies from the taxa included to test against the theories one
proposes. That's what makes it a test.

<You're guessing and you're guessing wrongly, speaking as one who has done the
work. I would be more convinced that these workers had done their work if I had
seen labeled tracings and reconstructions. Roadkills are devilishly mysterious,
until the CSI guys dissect the scene. Adding characters and taxa would solve
their massive MPT problem. The data is available. They just took the easy path
by adopting Kellner's work.>

  I have actually run and tested trees with about a million MPTs, for the sake
of dealing with 100+ taxa and 600+ characters. One still manages to get
surprising resolution. As for Lü and Ji, what Dave seems to have the larger
problem with, was that they did not include the various specimens he himself
treats as unique species. This is something to do at a stage in analysis, but
the authors instead were interested in testing positions of various Chinese
taxa. They were hardly out to make a complete study of all pterosaur taxa, and
they shouldn't be held to that standard if their goal was separate. Rather,
they were using one of the most complete pterosaur phylogenies published to
date and expanding it with additional Chinese taxa; hardly definitive. As such,
since it would appear they do not agree with the lacertiform hypothesis, they
are operating in an entirely reasonable framework. Since there are a few who
apparently strongly disagree, let them publish their disagreements.

<Not so here, my friend. Show me one study that has Rhamphorhynchus as a dead
end without sister progeny. It's always the last bus before the transfer.>

  There's no such thing as "sister progeny" in cladistics. ALL taxa are
"dead-ends" unless we're discussing cladistic lineage segments or pre-cladistic
"lineages". There is a problematic argument in treating taxa as having
"descendants" or "ancestors" when you can't tell the difference in a cladistic
structure between an ancestor and a sister group, even if that sister group is
ONE species.

<"I am sure" is a well-known weasel phrase for "I have room for for doubt but
don't want to express it." Better to leave out this phrase. And the postcrania
is not as plesiomorphic as you might assume. In my study, there isn't just one
Rhamphorhynchus, but a whole bush leading from Campylognathoides alone, with
lots of variation in every part of the body.>

  In this case, "I am sure" was used to state that "I see the postcrania as a
lot more plesiomorphic than the skull, there are others who agree with me--if
at least in general--but I won't name names."

  As for variation in the body, I tend to take such things as proportions that
I beleive Dave himself doesn't as variational and not taxonomically significant
in a whole. But that's my perspective, not one commonly shared. Not all taxa
are constrained in proportion, and one gets ontogenetic variation turned into
taxonomic variation when one splits a species into old and young specimen,
while at the same time treating the latter as valid species or competing for
the idea of specific recognition. Has Dave tested this with extant species yet?
I doubt it. Thus I bet this "bush" is the result of splitting juveniles into
species. Using adults only, one would likely get a different array, but then,
Dave thinks the juveniles ARE adults. So we'd need to wait for the paper to
modify the matrix such that juveniles are lumped into their parent taxa, or
simply omitted altogether.

<And for good reason. Sordes is a short-tooted type of Dorygnathus, as are all
subsequent pteros. Not the other way around, which is how Lü and Li portray

  "Subsequent"? More of that non-cladistic philosophy? *Rhamphorhynchus* is
derived from an earlier condition, and it is likely that while *R.* attained
its distinction wholly on it's own line, so too did other taxa. The more
similar some taxa are, the closer they likely are to that lineage "archetype".
In Lü and Ji, *R.* is positioned closer to other pterosaurs than are
*Campylognathoides* and so forth, but this does NOT mean it comes FROM *C.*,
only that *C.* branched off earlier than *R.* Both then have time to diversify
and develop autapomorphies.

<??? You've phrased that incoherently.>

  How so? I doubt Rhamphorhynchidae is very incoherent in the current
environment. Perhaps "environment" referring to the approaches and results in
study, as in a gamer's term, would be better understood if I indicated that I
used it as a gamer's term for a concept that fits the situation in which I was
using it. Incoherent? I don't think so, but perhaps so. Rhamphorhynchidae or
"Rhamphorhynchidae" may very well be polyphyletic, being comprised of serious
outgroups to a more monophyletic "Pterodactyloidea".

  I had written: "As for the polyphyletic treatment of some clades, one must
wait for testable, available results to consider claims of such oddity, if
indeed such would exist."

<Again, ???>

  Dave, your analysis, which you constantly refer to, cannot be used to refute
statements from published papers until you publish it. The polyphyletic
groupings you argue for (various origins for some clades) remain untestable,
yet you constantly talk about them. You claim something is bad, but don't say
why (save that you treat taxa as split far beyond anyone has ever done, and for
reasons that have been refuted both in print and online -- I am referring to
the various responses by Bennett and during the pterosaur embryo debacle, which
you, Dave, referred to as adult pterosaurs!) and then don't publish on the
subject yet continue to mention your analysis as definitive. "Put up," as
"they" say. 

<That's tradition and paradigm. Test them. No one has yet. Don't be afraid to.
It's not that much work.>

  This is the approach I hear from pseudoscientists, such as those who claim
that research will find the "chi" particle that makes feng shui a real science.
They claim that as long as we lok hard enough, we'll find the results we've
been looking for, and I say of course: it's called a self-fulfilling prophecy.
One will always interpret the results in such a way that conforms to their
pre-determined arguments. The topic of juveniles into adults has been argued
against for a long time now, years, and nearly every researcher who has
approached the topic finds them to be juveniles. The key criteria to refute
against their juvenility, such as finished bone, closed sutures and fused
epiphyses have yet to be found. Absence of carpalia and tarsalia, and of
course, the key features of disproportionately large heads and eyes, all
provide strong evidence of their juvenility. This has been published on, and
yet is ignored. This isn't "fear", this is "acceptance". Other theories to over
turn this require EVIDENCE, and as "they" say [again], extraordinary theories
require extraordinary evidence.

<Not so, small size was assumed to represent juvenile status and long-winded
explanations were devised to promote the idea despite changes in bone, tooth
and proportion that could just as easily, and it turns out, more readily, to
have been phylogenetic. If I were wrong, I should be the one with 34,000 MPTs.
Right? Right? No I have one tree, and all the sister taxa blend, like Mr.
Darwin said they would.>

  You mean, the study of ontogeny's application to the fossil record was
invented as a sham to prevent knowing about fossils? Gosh. Then where are all
the fossil juveniles? Are we to beleive that ALL fossil juveniles have wholly
cartilagenous skeletons that don't fossilize except as vague ephemera on some
slabs in lagerstaetten? The reason ontogeny is applied so well to the fossil
record, and a measure of its capability to explain nature, is because it does
so the same way in real life. Living animals and their ontogenies are applied
to dead organisms, and change is found to be absent. OF COURSE juveniles will
be smaller than adults, will appear to have less formed bone, and will lack
fusion between the bones, different proportions, and some special hallmarks
that appear to be true to ALL vertebrates in having a MUCH larger cranium
relative to body than adults, and in the face, larger braincase and orbits
relative to the cranium where present. It's when organisms or fossils depart
from this observation that scientists wonder and investigate. This argument of
ontogeny recapitualing phylogeny has been one of the most fundamental
biological observations for the past hundred years, and in its current form,
"evo-devo", serves to investigate the fundamentals of change in ontogeny
THROUGH evolution and vice versa. It's not that people don't WANT to look at
other possibilities, but that when the idea does come up, it gets trashed
because there is not enough evidence for it to overwhelm the evidence against
it. The same is true with Dave's theories of "ephemeral babies" and
"hermit-crab pterosaurs".

<Many discoveries, from continental drift to a heliocentric solar system, were
made by mad men working alone with various sorts pointing fingers and calling
names. And you, Jaime, are one of the sticks in the mud, as you'll discover

  See above on chi particles. Find them, then report them. Don't say the means
will be found, then reported, while at the same time furthering the opinion
that it's true without that evidence.

  And as for being a stick in he mud, sure. Whatever. I've participated enough
in pseudoscience debates to ask for the evidence that I find wanting, such as
in this case. I started this whole approach LOOKING for the data, and could not
find even what I was asked to find in photographs and casts of specimens. I
tested, and I found the hypothesis lacking in credential to be able to
withstand further tests. So have others, such as Chris Bennett, who's opinion
must also be delegated to "a stick in the mud" for not apparently "seeing"
these things. We have all asked for evidence, and received nothing but
refutation of other people's data, and this reminds me of the issue that was
going on in Kansas and Pennsylvania last year too much for me to back down on
further, similar arguments. Hypothesis of denial, sans positive evidence. When
asked to prove fossils are adults, it seems the only answer is this unseen
cladistic analysis, which is why many have asked for it, or have been waiting
for it, so as to test these claims. If this makes me a stick in the mud, at
least I am investigating the depth of that mud!

<Not for lack of trying. The strategy now is to publish and finished revision
of the Amniota, then work to the branches.>

  Why not stick to pterosaurs? It seems that for some people who spend decades
studying a small group of amniotes, an approach on ALL in a few years is rather
ambitious, especially without accessing the original fossils or casts.

<At the time, you'll remember, the specimen inside the eggshell was the size of
a typical adult anurognathid. It's still an anurognathid.>

  It's size is really irrelevant as a juvenile. An eaglet is larger than
virtually any hummingbird. The case was made that it was a juvenile and the
proportions appeared similar to some ornithocheirids, which was all testable.
Then came the claim that it was the size of an anurognathid, so much have been
an adult. No evidence for being an adult was given, especially when it was
pointed out the bone surface texture was "clearly" juvenile (or at least
insofar as ontogeny tells us it is juvenile bone texture). 
<Only a juvenile of a much larger one, only one of which is known in the adult
form. This is called making an honest mistake, which I was glad to announce at
the discovery of the second and third pterosaur eggs. Altogether this is called
progress. Or science.>

  Yet those authors, who may or may not have seen this "report" in what can
only be described as a hobbyist's and afficionado's magazine, disagreed by
calling them juveniles of other pterosaurs.

<I submit to you, Jaime, that the bits and pieces of the entire baby pterosaur
are present and visible inside of each egg. Actually, the bones are 'packaged'
rather nicely in their original containers. I have traced them. All the bones
connect as they should. The work has been widely available for years.>

  Okay, Dave, this seems misrepresentative of you. I should think we both know
that what I have been calling "ephemera" (as you yourself have taken up),
refers to other specimens, not the ones inside eggs. It has been challenged,
including by Bennett, that babies "seen" on slabs adjacent to "adults" of
specimens of Solnhofen pterosaurs were in fact non-ossified, "ephemeral"
juveniles. This followed the apparent "discovery" of such ephemera a year or so
earlier. NO ONE has challenged the existence of the embryos in eggs save YOU,
who called them adults.

<Yes, put your head in the sand and avoid testing when it would be so easy to
do so. And so rewarding. I encourage you to put any tiny ptero in a matrix and
see where it falls. A dozen would reveal more though.>

  Dave, I have tested your images, so has Chris Bennett, and so has David
Marjanovic. The latter two even have websites of being unable to find or just
plain refuting your discoveries.

<Removing the tiny pteros does indeed bounce the cladogram back to a ladder --
but then you have to deal with sister taxa that do not blend as Darwin said
they should.>

  So instead of looking at the gaps, we decide we have to revise the tree to
"blend"? Or do we look at the analysis and think to ourselves "Am I leaving
things out? Am I including all synapomorphies? Did I include so and so's data
on this problem taxon or that one? Did I include that specimen there?"

  Now, I am all for total inclusion of taxa and characters and specimens. But
common sense dictates that some characters are independant of phylogeny but
relate to ontogeny, and others to mass-relationships as an animal gets bigger,
just as robusticity (diameter of a bone versus its length or whatever
robusticity measure there is), making them problematic to include. Common sense
also indicates that juveniles, because of these ontogenetic or size-related
issues, will come out different than their adult counterparts, sure as juvenile
pantherines are more similar to adult felines. Many juvenile birds, to give
another example, have disproportionately larger feet compared to their wings
because they walk before they fly. Pterosaurs may be different or the reverse,
as in bats, which cling then fly, before they locomote otherwise. Pterosaurs,
indeed, nest, so they likely never clung, and given Unwin's work, appear to
have developed walking prowess after beginning to fly. And this is all

<There is something deliciously wonderful about lifting the veil of ignorance
and seeing unexpected truth after years of work. There is also something
devilishly charming about certain folk who play their part so well and create
unnecessary drama about such trivia.>

  You know, I would be blinded by the forest too if all I was looking at was
the tree. Sometimes you have to look at something with your eyes, then your
OTHER eyes, and then with your eyes again, before you see anything. More
Pratchett, sorry. Enlightened fellow, maybe.

  Point is, when you are sure you are right, you never really look for things
that make you seem wrong. You just deny them. They endanger your rightness,
after all. I have NOTHING to gain from this argument, on the contrary, save
that I hope that I can help people LOOK again at the things they've been
looking at with a different set of eyes. I guess that's what makes me a stick
in the mud.


Jaime A. Headden

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)

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