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



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with a much larger unpublished gamut.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. 

:  )

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.

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. 

________


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.


_________

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. 


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.

_________

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.

__________

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. 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. When I delete taxa down 
to match the lists of smaller studies I get their results, unless their 
character coding is really botched up, and I've seen that too. 

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. 

____________

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. 

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.

I need to buy you a beer, Bill. 

David Peters
St. Louis