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



On Apr 13, 2010, at 5:24 AM, David Marjanovic wrote:

>> 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.
> 
> Well, you sometimes give me the impression that you're frustrated at the fact 
> that nobody sits down and does a really big study. That isn't done because 
> it's just too much work, and you give the impression of not knowing how much 
> work a big morphological phylogenetic analysis is.

Still, it needs to be done. I did it. So it can be done. If not to your 
satisfaction, well, that's another matter. Is everyone still waiting for John 
Merck, who, I hear, is working on the same subject?
> 
>> 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?
> 
> Like what?
A host of herbivorous Permian amniotes with a lateral temporal fenestra and no 
upper temporal fenestra. 
> 
> I'm asking because I know a relevant, small, unpublished matrix (in press in 
> JVP, so I suppose it'll come out sometime next year).
> 
>> 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.
> 
> Well, no. You don't observe the specimens in person, you rely on the 
> literature, even though the literature often lacks descriptions or 
> illustrations of important body parts (which often only turned out to be 
> interesting decades after publication), even though the illustrations that 
> are there are often misleading about 3D relationships (this holds even for 
> good photos [pers. obs.], never mind line drawings!), and so on.

You stand by your statement "You don't observe the specimens in person."? That 
can be falsified by seeing one specimen in person. 
You stand by your statement "the literature often lacks descriptions or 
illustrations of important body parts". This can be falsified by several papers 
in which descriptions and illustrations of important body parts are included. 
You stand by your statement, "the illustrations that are there are often 
misleading about 3D relationships". This can be falsified by several papers in 
which illustrations are not misleading about 3D relationships. 
> 
>> 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.
> 
> No -- time to look at the specimens again. If the autapomorphies really are 
> weird, as demonstrated by the specimens, _then_ it's time to rethink.

 Thanks for agreeing.

> 
>> Bottom line, we both know
>> what we're doing -- most of the time.
> 
> Now that I've explained to you why potentially continuous characters should 
> be ordered, and what the difference between a matrix for phenetic analysis 
> and a matrix for phylogenetic analysis is, this is true (...I hope). 5 years 
> ago it wasn't.

Why would you pretend that I don't know this when I'm able to separate caseids 
from eupelycosaurs, etc. etc. while others are not? This is a red herring and a 
meaningless jab.
> 
>> 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.
> 
> But you can't _tell_ whether a tracing is wrong, unless you've seen the 
> specimen!

No one said "wrong". I said "poor" and half-baked" (=lacking in detail and 
precision, see above). Is this sort of misunderstanding of simple words at the 
root of our disagreements?
> 
> I've seen both published photos of the holotype skull of *Tseajaia* in dorsal 
> view (Moss 1972, Berman et al. 1992). It took me quite some time to grasp the 
> fact that they're both of the same skull; slight differences in angle and 
> lighting make them look utterly different, including the positions of sutures.
> 
> (...And then there's the disgusting habit of tracing sutures in ink _on the 
> specimen_ instead of on the photo. The skull in question has such ink on it, 
> and maybe the amount of ink changed in those 20 years.)

Interesting anecdote.
> 
>> Also, let's think about Vancleava again, and it's misnesting.
> 
> You keep telling us as a matter of fact that it's misplaced, when you haven't 
> even published your analysis.

WFTP
> 
> Look, we can wait for a year. There's no problem.

Then be patient. 
> 
>> 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.
> 
> I don't see how the second paragraph addresses the first. I don't see any 
> connection.

I'm indicating the sort of involvement  and resolution that Bill thinks is 
lacking. We've all seen trees with 500,000+ trees that get published. I would 
never attempt such a sham.
> 
>> 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.
> 
> There are other problems.
> 
> One is when people score an entire presumed clade as having a character 
> state, even when the character is unknown in some of the OTUs in question. 
> Happens a lot, as you can see in my 2008 paper in Cont. Zool..

Interesting anecdote. 
> 
> Another is when people throw out informative characters when they can only be 
> scored for a few OTUs. Mickey Mortimer can give you a long rant about that, 
> I'm sure.

Interesting anecdote.
> 
> A third is when a cell is scored as unknown because the literature doesn't 
> describe it -- but makes clear that the body part in question is preserved! 
> There are cases where I had to do this myself because I wasn't able to see 
> the specimen.

Interesting anecdote.
> 
>> 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."
> 
> You're both right. That is the tragedy.
> 
>> 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.
> 
> This is only "easy" and "simple" if the literature describes and illustrates 
> the necessary taxa unusually well or if you have the specimens at hand.
> 
>> I have done the work.
> 
> In a very, very, very sloppy fashion.

If you're going to insult my work, please have evidence and details. Otherwise 
it's just name-calling and you're better than that. I hope.
> 
>> And I am in a position to raise red flags.
> 
> Based on rather subjective reasons.

Again, you're insulting without evidence. Please provide details. 
> 
>> 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.
> 
> It's because you disagree with the descriptive literature so much. You 
> reinterpret fossils based on your own tracings of grainy photos -- I wouldn't 
> take issue with a single suture without having seen the specimen.

Your statement could be falsified by a single tracing of a non-grainy photo, or 
by personal examination of a single fossil, or one single reference to the 
literature. David, You might be painting with too broad of a brush. Typically 
that stems from prejudgement and that comes from some sort of perceived threat 
to a "natural order." 
> 
> In my abovementioned paper, I reinterpreted the homologies of a few skull 
> roof bones of the lysorophian "lepospondyl" *Brachydectes* without having 
> seen the specimen. But all I did was to exchange the labels on those bones; I 
> didn't change anything about the course of sutures, presence of foramina, or 
> whatever.

Interesting anecdote.
> 
>> To my point, the Amniote
>> phylogency submission simply provides the overriding study that has
>> been missing from Amniote studies.
> 
> The version I saw (several years ago, I hasten to add) was very sloppy. It 
> was chock full of correlated characters, all were unordered, the limits 
> between the states weren't explicitly justified and therefore 
> indistinguishable from arbitrary...

Details please. Otherwise others may think you're just trying to vilify.
> 
>> 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.
> 
> You're _not_ doing it. You're trying to get results without doing enough work.

Seriously, David, if you were correct this work would already be done better 
and by someone else. Where is your logic chip? Any amount of work trying to 
figure out the family tree of the Amniota as a whole, is better than what we 
have now, which is next to nothing. We have all the branches, and we're kinda 
sure how many go together, but the whole tree has not yet been put back 
together. If you know different, send the reference.
> 
>> 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.
> 
> Doesn't surprise me. How much resolution there is depends on the amount of 
> character conflict, and that depends on the absolute number of scored cells, 
> not the relative number of unknown ones.

> 
>> The work is already done and has
>> been done for several years.
> 
> No. Not only hasn't it been published, it's so sloppy it wasn't worth 
> publishing -- you didn't know what you were doing, you didn't know how 
> phylogene.

Something got garbled here, but I get your overall point. Again, David, if you 
want to avoid appearing as if you were just intent on insulting a person it 
would be better to have some specific evidence to consider. That way we can 
have a nice chat about that. Stay scientific, precise and polite and we'll 
figure this out together.

David Peters