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Re: PDF-request: Original description of Lagosuchus and/or Marasuchus



On Tue, Apr 13, 2010 at 12:33 AM, David Peters <davidpeters@att.net> wrote:
> Writer's note: For those not interested in wading through muck, there's some 
> light shed, I think, about 3/4 of the way down. Key word: "brass tacks".
>
>
> I wrote earlier:
>
>>Most systematic problems
>>written by recent Triassic workers have arisen from a priori taxon gamut
>>assumptions that have never been >fully tested, as determined from testing
>>with a much larger unpublished gamut. Differing >observations of character
>>traits are only the final "sanding" of a structure that has (typically, >but
>>not always) already been built.
>
> Bill Parker wrote:
> I find this statement somewhat snarky.
>
> No need to assign negative adjectives. No one's being snarky here. :  ) 
> There's no "tone" >to this other than mild frustration at the recent glut of 
> cladograms with generally fewer than >twenty taxa, many supraspecific and all 
> selected a priori with no overriding study to support >these choices.

If you want to test ingroup relationships within Archosauria then you
include all known hypothesized archosaurs (preferably as individual
specimens and/or species) with a few closely related taxa (based on
synapomorphy) as outgroups to polarize your characters.  Isn't this
what has been done?  Your hypothesis is that some of these taxa are
not archosaurs and you are free to test that.  If you can support
non-archosaurian pterosaurs and lagerpetids then that is great as far
as I can concerned.  [As an aside you have to use some supraspecifics
(e.g., passerine birds) or you would create an unwieldy dataset, but
three taxon statements to represent 'families' will work nicely] .

>
> :  )
>
> To that point: You know as well as I there has never been a large cladistic 
> analysis that has encompassed a large gamut of amniotes. So the presumed 
> subsets within the Amniota >have no real and tested basis for their 
> appearances, other than tradition and a priori >assumptions. Case in point: 
> Why were caseids lumped in with eupelycosaurs when there >are plenty of other 
> taxa out there that have more in common with caseids? My point is this: >if 
> science is so important to you, and I know that it is, then anything (like an 
> inclusion set) >based on tradition and opinion is, by definition, 
> unscientific.

True, the subsets were developed using non-phylogenetic methodology,
but still on the basis of shared characteristics.  Current workers are
still determining if these are synapomorphies or homoplasies.  Of
course the eventual goal is to create all inclusive phylogenies of
major groups of organisms; however, most workers seem to feel that
this is currently premature.  Caseids may share lots of characters
with lots of different groups but which characters reflect true
phylogeny and which are simply convergent?  How does a large dataset
with all tetrapods determine this better than a smaller dataset of
only synapsids?


>
> Bill Parker wrote:
>
> Remember not only is the literature written from >first
> hand observation< (and this itself is a major assumption), but also
> from the authors personal interpretation of that observation.  This
> interpretation can and has often been influenced by factors such as
> poor preservation, bias based on preconceived ideas, subjective
> judgement of homology, misidentification, and sadly in some cases
> deliberate deception.
>
> Not sure why you feel the need to preach to the choir here. This is what I 
> base all my papers on.
>
> ________
>
>
> Bill Parker wrote:
> No.  First hand observation is crucial.
>
> Yes and no. See Bill's notes about preconceived ideas, etc. above, which 
> support my >POV. No, testing is crucial. Do the observations create weird 
> autapomorphies? If so,  time >to rethink. (Sorry, now it's ME who's preaching 
> to the choir. ) Bottom line, we both know >what we're doing -- most of the 
> time. We all need each other to point out problems so we >can repair them. 
> That's why I raised my hand when the Vancleavea paper came out. Too >many 
> weird autapomorphies and too small of an inclusion set from a team of 
> first-hand >observers. And, yes, I've NEVER seen the fossil, but I know 
> problems when I see them.

But autapomorphies tell you absolutely nothing about phylogeny.  But
autapomorphies tell you absolutely nothing about phylogeny. But
autapomorphies tell you absolutely nothing about phylogeny. But
autapomorphies tell you absolutely nothing about phylogeny.But
autapomorphies tell you absolutely nothing about phylogeny.But
autapomorphies tell you absolutely nothing about
phylogeny...........do I need to say it again? :)

Vancleavea has numerous Archosauriform synapomorphies as well as a
gamut of vertebrate plesiomorphies.  As systematics we are interested
in how high in the tree the synapomorphies place us.  Where do you
think Vancleavea is a better fit and based on what synapomorphies?


>
> ________
>
>
> Bill Parker wrote:
> There is absolutely no alternative for seeing the actual specimen.
>
> Yes and no. We've all seen poor and half-baked tracings of specimens that 
> clearly could have been handled with more care and precision. Such tracings 
> reflect the thinking of the observer, sometimes in a rush to get things out 
> and published. Also, let's think about Vancleava again, and it's misnesting.

You have to see the actual specimen to remove any subjectivity
introduced by another workers interpretation of the data. But
autapomorphies tell you absolutely nothing about phylogeny.But
autapomorphies tell you absolutely nothing about phylogeny.<broken
record>  How else could you be certain you are providing the best
support for your hypothesis?

Why is Vancleavea misnested? Based on what? The most derived amniote
clade we can place it in based on synapomorphy is archosauriformes.
Why is that a problem?

>
>
> _________
>
> Bill Parker wrote:
> Sure the algorithm can
> handle the large dataset and spits out a tree, but phylogentic
> analysis is much more involved than data entry based on simple
> observation.
>
> Again, Bill, you're trying to make it sound like I don't know this. My 
> cladograms end up with a single tree and some are built upon 40,000+ data 
> points. Subsets are also single trees. Any test you want to use on these 
> trees you can use.

This statement sends up a red flag to me. It is pretty well
established that random analysis provides single MPTs on the basis of
noise which does not replect true phylogeny and which in fact presumes
complete data congruence and no homoplasy.  You do realize that this
is extremely unlikely for such a large dataset as the one you propose?
 Is it possible? yes.  Likely?  no.

How do you know your data have not been randomized because of the
historical relationships of such a wide gamut of taxa and characters?
What tests have you performed to distinguish truephylogentic signal
from random noise?

>
>
> Bill Parker wrote:
> …adding taxa is also
> something that needs to be done carefully given problems with 'missing
> data', utilizing species vs. supra-specific terminals, etc..
>
> We all know these things, Bill. I've been preaching to the list about the 
> dangers of supra-specific taxa for years. Missing data? That's a red-herring. 
> You already know you can add a skull, a pelvis or a foot to most cladograms 
> and get pretty close to a correct nesting.

Agreed, missing data is a red herring, which is why I put it is
quotes; however, it still needs to be considered as it is related to
the wild-card taxon problem, which do reduce phylogenetic resolution.

>
> _________
>
> Bill Parker:
>
> Rejection of manuscripts should never be
> based on results but rather on flaws in methodology.
>  If your methodology is sound and repeatable then it should be published no
> matter if the results are unorthodox.
>
> So, these are the brass tacks. You've been railing against my methodology. 
> And I've been >railing against yours. You say "You must see the fossil or be 
> rejected!" I say, "You must >include all pertinent taxa in your tree or 
> you're going to get 'by default' nestings." If you >have an opportunity to 
> referee my paper, you will probably reject it based on your >paradigm. I 
> would do the same to yours if I saw systematic problems. My protest of your 
> >methodology is easily handled by simply adding the necessary taxa as a test 
> to see if your >topology remains the same. Your protest over my methodology 
> is easily tested by >something like Vancleavea. That case is not closed yet.

Adding taxa always changes topology because by definition adding taxa
adds internal branches.  That in itself is not a test.  The test is to
find a taxon that shares more synapomorphies with Vancleavea than ones
that have been proposed.  I would certainly embrace any relationship
which passes this test as would any phylogeneticist. How does one
recognize a "systematic problem" in your definition?  I think that you
mean poor taxonomic sampling and I would agree.  How would you propose
determining what you call "necessary taxa"?

>
> __________
>
> Bill Parker wrote:
>
> I'll be honest here....I've interpreted the tone of some of your
> messages as implying that you already know all of the answers, you are
> just waiting for the rest of us to catch up. This last message was no
> exception and again, if you are the one who is questioning all
> previous results, then you need to develop the alternative hypothesis
> based on sound technique and repeatability.  You may be right, but
> currently your criticisms and stated results are not testable thus not
> scientific.
>
> I'll be honest, too. I have done the work. And I am in a position to raise 
> red flags. My >submissions on Amniote phylogeny have been rejected because, 
> to your point, I have not >personally visited all of the specimens, even 
> though that has never been a requirement in >other phylogenetic work of this 
> size (and magnitudes smaller) from other workers and no >one has ever tested 
> the assumption that personal observation would be so superior to >pulling 
> data from the literature that it would change tree topologies.

IMHO rejection on these grouds would only be prudent if the reviewer
could demonstrate that many of your codings were erroneous and that
direct examination would fix this problem.  Of course, wouldn't you
have wanted to check this before you even submitted?  This is a common
problem in many analyses.

>To my point, the Amniote phylogency submission simply provides the overriding 
>study that >has been missing from Amniote studies. Without an overriding 
>study, all subsets are built >on tradition and guesswork. To your point, my 
>work can and should be tested but it can't >be tested until it's published. 
>Referees who reject it are evidently happy with the various >mysteries that 
>could be answered with an overarching survey. I've tested it any number of 
>>ways.

I don't think anyone has a problem with overarching surveys.  They are
just very difficult because of the expanded dataset and prone to give
misleading signals unless everything is coded absolutely perfectly and
characters are perfectly constructed.  Furthermore, how can you test
your signal without utilizing studies of subsets, especially when
according to your statements these submatrices get different results
because of reduced taxon sampling?

>When I delete taxa down to match the lists of smaller studies I get their 
>results,

Even with your expanded character set?

>unless >their character coding is really botched up, and I've seen that too.

How can you confirm botching without seeing specimens firsthand?

>
> There's no glory in subjecting myself to your adjectives about my character, 
> motivations and emotions. I do this because I'm only after one thing: what 
> we're all after

We are all after the same thing, robust phylogenetic hypotheses;
however, to repeatedly claiming that no one else is doing it correctly
necessitates that you clearly demonstrate why this is so and provide a
well-supported alternative hypothesis.

>
> ____________
>
> Bill Parker quoted and commented here:
>
> On Sat, Apr 10, 2010 at 12:11 PM, Jaime Headden <qi_leong@hotmail.com> wrote:
>>
>>   >   So what I got from both Mike's and Bill's replies to your arguments
>> vis-à-vis >*Trialestes* was that 1) literature is not sufficient for some of
>> the information one might >want to question phylogenies, 2) much less
>> construct them, and that 3) simply having other >people do the work for you
>> is going to result in a lot of waiting time, meaning 4) it's often >better to
>> do the work that you need to have done yourself.
>
> BP: Bingo!
>
> Well, there's a lot of fingerpointing here, IMHO.
>
> Getting back to evidence: Trialestes is indeed not well known in the 
> literature. But enough has been said about it to add a few characters to a 
> matrix and see (test) where it comes out. Lots of missing data, true, but not 
> enough to have a loss of resolution, interestingly enough.

I wish it were that simple; it's not just about missing data but an
overall lack of synapomorphies preserved in the material.

>
> Wondering now, which other people are doing "the work" for me? I don't 
> understand this >statement. The work is already done and has been done for 
> several years. If you don't >want to play, don't play. I was just interested 
> in some friendly discussion like, who's better >the Cards or the Cubs? That 
> wasn't too snarky, was it? I'll know better next time not to >bring up such 
> topics.

We are all playing, just not all on the same field yet.  Hopefully
there are some things we can all agree upon and just to emphasize a
key point again.....But autapomorphies tell you absolutely nothing
about phylogeny. ;)

>
> I need to buy you a beer, Bill.
>
> David Peters
> St. Louis
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