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Re: Wukongopterus and Darwinopterus

On Nov 27, 2009, at 3:42 PM, Mike Habib wrote:

> On Nov 27, 2009, at 8:23 AM, David Peters wrote:
>> When the tree topology is correct typo corrections will support the tree. 
>> When not, typos will correct a tree. The correct tree is/was out there. It 
>> just has to be echoed in analysis.
> Hypothetically.  Realistically, though, we will never have the "right tree" 
> for any given group - every topology will be inaccurate in some detail (if 
> nothing else, we don't have all the species that ever existed).  Therefore, 
> in all likelihood, every topology is "good" in some places and "poor" in 
> others, and how typo corrections will affect the various parts of the 
> topology is much more complicated than it might seem (if nothing else, how do 
> you know what got "better"?)  If you're getting the "right" tree with typos, 
> then you're getting the right thing for the wrong reasons, and there's 
> actually no way to tell that you were close in the first place.  In the end, 
> the only thing to do is correct errors as they are identified: typo-free is 
> always better, regardless of what happens to the tree.

I don't buy it. There is a single tree out there. It brought us all the 
specimens we now know. Every right tree we hypothesize will admit new taxa as 
they are discovered with no change to the rest of the tree topology. That can 
be tested. That's how you know. Everything else is philosophy and keeps players 
on the bench. Quietly get out on the field, test what you have and let us know 
what you find. Getting closer and closer to the The Truth should be the push. 
As good sports, we will declare your hypothesis the winner if it explains data 
better than any other hypothesis. 
>> Correlated characters? How difficult to determine: 1) long neck vs. long 
>> tail on sauropods; 2) short manual toes vs. short pedal toes on stegosaurs; 
>> 3) wide skull vs. orbits on skull roof on batrachomorphs; 4) number of 
>> caudal vertebrae versus loss of teeth in birds, etc. etc. etc. The list is 
>> endless.
> Yes, the problem is difficult.  However, presuming that traits are not 
> correlated because we do not wish to deal with the complexity is not the 
> right solution.

You're never going to figure out the perimeter of England because you come up 
against fractals. This complexity you're suggesting is another facet of 
fractals. Avoid it or delve into madness. All we're looking for are simple 
models for complex processes taking millions of years and just as many 
>> ordered vs. unordered: so difficult to determine with convergence and 
>> parallelism. Just look at any misnested taxon.
> How do you know they're misnested?

The list of apomorphies is enormous!  Just look at any Christmas card with a 
dog or an iguana as part of the family and you tell me, which one was NOT born 
in a hospital and wore diapers? 
>> Best to just let the suite have its say-so if there's any question.
> Presuming you mean everything should be unordered and ignored for 
> correlations, there are quite a few manuscripts in the cladistics literature 
> that suggest otherwise.

Posting your question back to you: how did they know they were more right than 
wrong when they concluded? 
>> In my experience, taking another look at MacClade when loss of resolution 
>> occurs, always exposes the misrepresented characters score.
> If you find misrepresented characters, then that's a good catch.  However, 
> low resolution does not mean a tree is "bad".  Sometimes, low resolution is 
> the correct answer given the data at hand: it simply means that taxa cannot 
> be differentiated in a repeatable manner according to the present data.  That 
> may be the error-free, robust answer for a given dataset.

Then get more data. It's always there. 
>> Evolution abhors apomorphies, preferring parsimony.
> Really?  News to me.
Mike, I hate to break it to you, but you like kinda like your parents and your 
grandparents. If you have a tail or fins or horns or gills, you hide it well.

>> Apomorphies do exist. They're just rare and like feathers, nearly always 
>> shared by "birds of a feather."
> Rare?  News to me again.  And yes, obviously the shared ones (i.e. 
> synapomorphies) are particularly interesting, but  I'm not sure where you're 
> going with this.

> Please name any apomorphy that is not rare. By definition any apomorphy will 
> be rare. 

>> Also, a good, healthy tree of sufficient size can sustain many dozens of 
>> typos, if not all concentrated near a weak branch.
> Is this based on a particular simulation study?  Obviously, if a tree is very 
> large, and contains six or seven typos, then the errors are a smaller 
> percentage of the dataset than in a case where the same six or seven typos 
> exist in a small dataset.  However, I'm not sure what this means for 
> "sustaining" typos, or how a matrix with many errors would still be 
> considered healthy.

Typos are to be avoided, but they don't ruin trees of sufficient size, as you 
indicate and agree with. 

>> "Weasel" words (i.e. could, can, might, may, would, should, possibly, 
>> recheck the quality, correlated, heterodox, believe, etc. ) are signs that 
>> specific data are being side-stepped.
> Actually, they're signs of uncertainty, which is a pretty basic aspect of 
> science, and therefore a common issue.  Yes, sometimes such terminology 
> indicates a cop out.  Often, it is just being realistic.  (Are bats closely 
> related to primates?  Well, the *might* be, as some trees support that - but 
> most trees these days don't, so it's *likely* they do not - this is just a 
> realistic assessment of the situation).

Good example. Test it. I have. I know the answer. AND YET, if someone else 
tests it and comes up with a better answer, I will gladly fold and declare a 
winner. That's science. 
>> "An apple a day keeps the doctor away" is a falsifiable statement. An apple 
>> a day (can, may, is believed to) keep the doctor away" is not. I trust no 
>> referee who relies on weasel words when falsifiable data is on the table.
> Which falsifiable data are in question in the present case?

An apple a day (0) keeps (1) does not keep the doctor away. Go straight to the 
verb and start eating one apple a day.   :  )



> --Mike H.
> Michael Habib
> Assistant Professor of Biology
> Chatham University
> Woodland Road, Pittsburgh PA  15232
> Buhl Hall, Room 226A
> mhabib@chatham.edu
> (443) 280-0181