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re: D.Marjanovics repliesto J'r pts I-II



Dave Peters (davidrpeters@earthlink.net) wrote:

<David, David, David. Please show me one cladogram in which all of the
specimens included were personally examined. Certainly _not_the case in
Unwin (2003) and Kellner (2003). They confessed as much. And if the reader
knows going into the manuscript that data was obtained in a variety of
ways, what's the problem?>

  Others have chimed in on this, but I will put my two cents in, as I have
a slightly different perspective than either Marjanovic or Mortimer do.

  Essentially, NO ONE can reasonably examine each and every specimen they
would like to include in their study. It's POSSIBLE, which means there
should be an honest effort to see as many specimens as you can, but NO ONE
can be possibly REQUIRED to examine them all prior to publication. This
leaves previous literature and proxy examination, e.g. photos, of the
material in question. It won't answer some questions (personal examination
may allow one to determine plaster or matrix from bone, as the case is
quite vague in *Huaxiagnathus* and has led to erroneous codings of both
*Nanotyrannus* and some other tyrannosaur specimens, including the FMNH
*D. torosus,* *Allosaurus* specimens, and so forth -- speaking on a purely
dinosaurian level; Bennett claims the preorbital crest in some specimens
of *Nyctosaurus* are plaster recons, and one would end up coding according
to such authority), and it may end up causing more confusion than before
(when using the literature, two different authors may code the same
specimen as having two entirely different states of the same character, as
in some conflicts in codings between Sereno and Holtz, etc.; so at which
point do you make that arbitrary descision to select one coding over the
other?). But this IS a temporary proxy, indeed: no analysis is intended,
nor should it be, to be THE analysis. There is always NEW data that will
change the previous analysis.

<Maybe you ought to try to publish it. After all, it's only data.>

  Verifiability is the issue, here, and why Marjanovic is loathe to do so.
This is why my own work on oviraptorids is so slow: to continue, I MUST
examine the material, in order to verify or falsify hypothesis I have
available to me or have formed (I wrote an abstract to SVP in 2001
relating to the kinesis of oviraptorid skulls when I felt I had enough
information to show that bending planes in some bones and joints between
others offered a unique form of prokinesis, but I have yet to actually
develop the data to verify this, and thus to my critic's eye, make it
available for the public ... I jumped the gun with the abstract, and
regret that, changing tactics with my intended theme [egg-eating] which
lead to the 2002 abstract in supporting H. F. Osborn and falsifying Norell
et al. in saying oviraptorids were not primarily egg-eaters -- there are a
lot of reasons, I would think, that shows they are) which would not
require as much "on the spot" positive data as the first does. This would
thus relate to phylogeny, provide valuable characters ... and CANNOT be
done from photos. If Chatterjee just SAYS we have a keeled *Protoavis*
sternum, maybe we should just plug his taxon in, because even though
others say its a chimaera, it's all anecdotal ... NO ONE has actually
tested the chimaera hypothesis, as even Witmer's review in _Above the
Heads of Dinosaurs_ was limited on the subject.

<Not the point. What they wanted and what they got was the point. And yet,
maybe a little more work would reveal the single tree. After all, Nature
is a single tree. I say don't publish until you have a single tree.
Otherwise you're showing your lack of ability to finish a job and do it
right.>

  What they wanted was the most resolved tree from the input of their
data. Several parsimonious positions available. This usually relates to
missing data, variance in characters, etc. How many characters does Dave
Peters code as "?" when the material is actually preserved, but the
condition ambiguous? Most authors plug in "?," but some may arbitrarily
decide it's "1" or "0" because that taxon _looks_ like another, making an
a priori coding descision. It should be a posteriori.

  Nature may be ONE tree, but like Marjanovic's example, it is currently
NOT possible to plug in the vast majority of extinct life that would
complete it. As it is, lineages HAVE been lost, may never have been
preserved, that are CRITICAL for resolving node conflicts in recovered
organisms or living animals, based on that little thing called the
"preservation bias." Lagoonal facies in the Bavarian forests are eroded by
the water and wind of southern Germany, so we loose potentially 90% of the
*Archaeopteryx* that died in the lagoons and were preserved intact (note,
90% is a HEALTHY estimate, far above the likelihood of the actual number),
thus underscoring their actual diversity, etc. Because of this it may be
likely that EACH of the specimens recovered may represent a different
species, because WHO KNOWS, the variation in and among the specimens may
very just relate to actual variation among species. So far, EVERY specimen
has been named as a unique species, some with just this such variation in
mind. However, if these specimens are assumed to belong to a single cline,
 showing ontogenetic and individual variation (some  specimens have
SLIGHTLY larger limb bones than larger specimens) it is equally possible
they all represent a single species. It does depend on the lumper/splitter
personalities, and both are equally viable. So ... test test test. Don't
assume there is only one possibility, and that only one tree can ever be
the likeliest answer, as it is most possibly likely you are kidding
yourself (this is not pointed at Dave Peters, but in general).

  BTW, one might look at life as _fractal_ rather than unified. There is
not ONE trunk, though at low resolution ("orders" versus "genera") one can
certainly see single stalks forking from thicker stalks, and so forth; but
there is likely a complex interbranching and "re-merging" of lineages at
the population level, that expand outward, so that the "true" tree of life
has at its core and along every divergent lineage a reticulated, "woven"
or net-like sructure, where only genetic isolation prevents reintegration
of the gene pool and a "true" split occurs. Thus, when one finds a tree
opne may be finding just one direction along a lineage, and another tree
with ONE different position may show resolution along another lineage; the
amount of genetic change or evolutionary acquisition may be "higher" on
one side than the other, resulting in more characters noted in one way
than the other. It's almost quantum.

  Thinking one has just one tree and that the analysis is therefore better
for it is almost like thinking one has found a religious "holy grail,"
something sought after but that no one ever really expects to find. But
it's the journey, as they say, that is the adventure, not the ending.

  Cheers,

=====
Jaime A. Headden

  Little steps are often the hardest to take.  We are too used to making leaps 
in the face of adversity, that a simple skip is so hard to do.  We should all 
learn to walk soft, walk small, see the world around us rather than zoom by it.

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


                
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