Re: Phylogenies, science, tea-time and more...

[FlxLandry@aol.com]

Hi again!

David wrote:
>> Enough  for an introduction. I was reading the discussion following Nick's
>>  intervention in favor of getting rid of silly postcranial characters  and
>> fragmentary taxa in theropod phylogenetic analysis, and was  suddenly 
>> cought by  the need of telling what I think about all  this.

>I hate to spoil all the fun... but apparently someone needs to  kill the 
joke 
>by explaining it: Nick is parodizing the way ornithischian  phylogenetics is 
>almost always done. By applying it to theropods, he  demonstrates what 
>nonsense results when one only puts a few skulls into  one's matrix. He is 
>crying desperately for someone to do a serious  phylogenetic analysis of 
>Ornithischia. (Probably he'll end up doing it  himself, alone.)

Ouch. I really am stupid. Well, at least it seems I was  not the only one to 
get cought, or all this list is just one vast  conspiracy...

>> It certainly was a good  thing to
>>  nuke the old crumbling linnean tree and get rid of "thecodonts" and
>>  "carnosaurs", which were mostly synonyms of ignorance.

>Unfortunately  (IMNSHO), the name Carnosauria was _immediately_ reintroduced 
>to  designate the sistergroup of Coelurosauria (...a name that should have  
>been dropped as well...). So, while *Tyrannosaurus* and *Megalosaurus*  are 
>no longer carnosaurs, *Allosaurus*, *Carcharodontosaurus*,  *Sinraptor* and 
>*Monolophosaurus* are still carnosaurs.

Yep,  that's one thing I know! :-) Anyway I don't think it's a bad thing that 
old  names are redefined under cladistic rules (you seem to disapprove the 
continued  usage of the term Carnosauria), and kept in usage, although I admit 
respect for  historical usage might lead to two quite different directions: 
save the name  whatever it comes to mean or nuke it whenever it doesn't 
correspond to its  original meaning... Well, if we must rename every clade 
every time 
the phylogeny  shifts around, we really are in trouble. But that's not really 
what I was  talking about.

>> I know this also depends on money, research  credits, and anyway
>> everydoby  wants to be as modern and up to  date as possible... But I dare 
>> to think
>> this is   NOT science. For me, dinosaur paleontology is mostly anatomy,
>>  stratigraphy,  paleobiology and paleoecology. The first two items are the 
 
>> dry and hard
>> data on  which the other two more  attractive ones are based.
>> But where does phylogenetic systematics  fit in there?

>It is based on anatomy, it is partly based on  paleobiology, and 
paleobiology 
>including -ecology are partially based on  it.

Ja! But the problem is that in a large part of current dino research  anatomy 
is no more than a tool for building some matrix, that, stuffed into some  
computer program, will release the new version of a phylogeny, just to be  
destroyed two months later. I'm not saying cladistics are coming from nowhere  
and 
pointless, just that they seem to be a little bit too overriding these days.  
And I do think (but I have no experience, so this could be complete nonsense)  
that a deep knowledge of anatomy should be something a human brain can cope 
with  well enough to identify phylogenetic relationships, first at species 
level, and  then higher up. After all, most of the important dinosaur clades 
were 
identified  well before cladistics, on a morphological basis. 
Now I know  interrelationships among these groups are quite tricky to figure 
out, but I'm  not convinced that a whole bunch of, say, maniraptor 
phylogenetic analyses are  better than one thorough anatomical, computerless 
comparative 
study of basal  members of the various maniraptoran clades. That's largely 
what cladistic  analyses want to be, but frankly, saying that A is more closely 
related to B  than to C because it shares 5 apomorphies with the former and 3 
with the latter  doesn't look like a reliable method to me. It works very fine 
for massive  phylogenetic evidence, like "tyrannosaurs are coelurosaurs", but 
when we get to  more subtle aspects or fragmentary specimens, constant and 
massive changes in  the results of analyses show that they're not that useful.

>> But  after this is done, I can't see the sheer utility of  those numerous  
>> analyses.
>> You add some abscure species known from  two
>> teeth and  one caudal vertebra and the tree gets completely  changed... 
Get 
>> rid
>> of some  characters you don't  like and Corythosaurus might appear as a 
>> brand
>>  new  ankylosaur!

>If your tree is so unstable, you clearly have  far too few characters*, and 
>probably too few taxa as  well.
>
>* Get a look at the "Basal Tetanurae" chapter in The  Dinosauria II. The 
>analysis in there has 638 characters. It will teach  you what I mean by "too 
>few characters".

Not "my" tree. I don't  have any. I'm now old and experienced enough to know 
that I'm very far from  being competent enough to pretend tackling any serious 
phylogenetic work on  dinos, although the time may come some day... I'm just 
seeing that most new  papers imply some new tree, and that there's no real 
reason to, at first glance,  believe someone in particular is right. A 600-more 
characters analysis means  that the researcher(s) (I'm still waiting for my 
copy of the book, should arrive  in a week or two...) behind have real in-depth 
knowledge of the anatomy of the  beasts they're talking about, which is usually 
not the case, just because that  research has not been done for most new or 
little-known species. Then, in any  cladistic tree, if some topology is weakly 
supported, then it cannot really be  trusted. If it is strongly supported, 
then the cladistic method probably wasn't  necessary to find it out. I'm 
absolutely not against cladistics. I just indended  to mean that there should 
be more 
detailed anatomical study, and less quickly  done analyses. A really 
meaningful phylogenetic analysis, just like a really  thorough anatomical study 
(when 
dealing with a reasonably large group or  reasonably well preserved bunch of 
specimens), used to imply a monograph, or at  least a long paper. These are, I 
think, invaluable, and all the more necessary  as we find new species.

>> I think Nick is right at pointing   that part of the rampant phylogenetic
>> instability comes from  including too  fragmentary taxa,

>Ironically, missing data are  usually much more harmless than one might 
>think. There are theoretical  studies on this to supplement my personal 
>experience (and doubtless the  much richer one of others).

I would naturally tend to think that missing  info is harmless, but how many 
times have I seen (mainly on that list, I have to  admit) trees shifted by the 
inclusion of some fragmentary bits and pieces...  Anyway, what I meant is 
that once cladistics have determined, say, where do  tyrannosaurs fit in the 
theropod tree, and the general pattern of tyrannosaur  interrelationships, if 
some 
new species is described from just one incomplete  specimen, then a 
discussion on its phylogenetic position, based on careful  examination of what 
is known 
(I mean, an actual TEXT about that), should work  just as well, or better, 
than a computer calculation.

>> but  doesn't it come also from inadequate study of those
>> reasonably well  preserved specimens we have at hand?

>Of course. My bird matrix  
>http://www.unet.univie.ac.at/~a0000265/cladogram.htm is an extreme case  of 
>this. I haven't seen any of the specimens I've coded there, I have  relied 
>completely on the literature which is often very superficial. By  examining 
>the specimens -- or reading good monographs on them, which  don't exist -- I 
>could perhaps cut the number of question marks in half.  (That's the most 
>important reason why I don't consider it publishable --  even though I fear 
>it is better than any published analysis of Mesozoic  birds, for example in 
>the sheer number of taxa that aren't included  anywhere else).

Seems like we're quite much agreeing in  fact...

>> As a student in social sciences, I have got quite a good  knowledge of the
>> good and bad points of quantitative and qualitative  methods. Cladistics 
>> are a
>> quantitative method,  everyting being based on the NUMBER of shared 
>>  apomorphies,
>> and the like. When reading sociology works, I tend to  strongly dislike
>> studies  based on pure statistics, while I  believe interviews of "real" 
>> people are
>> often   thrilling. Is it that silly to say that we could somewhat turn 
back 
>>  to
>> actually  thoroughly interviewing fossils instead of  comfortably use some
>> unreliable  statistical  method?

>I don't think this metaphor works. In sociology you have to  cope with 
plenty 
>of phenomena that are not quantifiable to start with.  In morphology, those 
>are rare... and actually just causes of ignorance.  An example is the 
>question whether a particular character should be  ordered, and if so, in 
>which way, or even which characters to include in  the analysis at all. 
>Learning more about the ontogeny, inheritability,  variability etc. of the 
>character in question (and on its dependence on  other characters!) can 
force 
>us to exclude several possibilities,  ideally all except one. (Unfortunatel
y, 
>papers on phylogenetic analyses  rarely explain the choices that were made 
in 
>coding.)

Here I  definitely don't agree. First, the bearing of quantification and 
statistics on  sociology is huge, although it's dwindling. But that's not the 
point. You can  indeed quantify many morphological traits, but 1) I'm not sure 
quantification is  the best way to approach morphology (that is, to do it well, 
you have to know  all those other variables you've just cited, and to explain 
how you use them),  and 2) well, see just below...

>BTW, I wouldn't call parsimony  statistics... maximum likelihood and 
>especially Bayesian methods do use  statistics... and as long as we aren't 
>talking about molecular data of  taxa with long branches, I wouldn't call 
any 
>of them  "unreliable"!

The thing I can't grasp about parsimony is why one femur  character and 
another cranial one should have more weight than one single  vertebral one, for 
example. I feel cladistics are sometimes a bit like asking  "are American 
democrats or republicans?", and answering that according to the  last elections 
it's 
most parsimonious to conclude they're republicans. I know  that this is a very 
rough caricature, but anybody working in cladistics is  confronted to just 
that kind of problem. By the way, what are "Bayesian  methods"?

>> And, more generally, is it really more  interesting
>> to know  where Torvosaurus fit on the cladistic  tree than to
>> know what it looked like and  how it  lived?

>This is a false dichotomy! If we don't know its place in the  tree of life, 
>we _cannot_ find out certain aspects of what it looked  like and how it 
>lived. "Nothing in evolution makes sense without a good  phylogeny."

Is it not supposed to be the other way round? How can we  figure out where it 
fits on the tree if we don't previously know what IT is,  independantly of 
phylogeny? You don't need to know whether a cat is closer to a  dog or to a 
mouse to what a cat is, how it behaves, etc... As far as I know,  knowing that 
tyrannosaurs are closer to birds than to allosaurs did not improve  in any way 
our understanding of how tyrannosaurs lived. We keep interpreting  them just as 
if they had kept being "carnosaurs", giant theropod predators, and  I think 
we're right about it. Evolution is one thing, knowledge about one  particular 
species or ecosystem at one given time is another.

>The  best thing about cladistics is that it has introduced  tree-thinking.

Right. But it also tended to nuke down grade thinking,  which was also very 
informative, not from a phylogenetic point of view, but from  a conceptual one. 
Herbivory is not a phylogenetic group, but it's a hell of an  useful notion 
if you study an ecosystem... I do love tree-thinking. I just think  it becomes 
bad, just like any other way of thinking, when it becomes omnipresent  and 
overriding.

Now I wonder how I can write so much silly things to  answer a reply that I 
largely agree with... Well, maybe it's too late for me  here in France...

Bye,

Félix Landry