Tuesday, August 31, 2010

Presenting the picture

We have seen that the Senter scatterplot completely contradicts the standard dinosaur to bird idea. The supposed path from dino to bird wanders all over the place between unconnected groups.
So how does the scatterplot relate to the ideas that I have been presenting?
First we would remove the Tyrannosaur cluster since it is not related at all to the origin and development of birds. We are left with the "Birdlike cluster" and an assortment of other unconnected groups.
According to the hypothesis I have been presenting, the Birdlike cluster developed from the pterosaurs, which unfortunately are not shown on the chart. So we cannot analyze that aspect of the subject.
But we can consider the relationship of the Birdlike Cluster to the other groups such as the Oviraptors, Alvarezsaurids, Therizonosaurids etc.

What I have been presenting is the idea that these groups developed from the flying birds within the Birdlike cluster. They are SECONDARILY flightless.
The reason that they appear morphologically unconnected in terms of the scatterplot is that they are as different as flightless birds are from flying birds. And there is no way in practice to distinguish intermediates because if a bird fossil is found - it is identified as either one or the other.

Friday, August 27, 2010

The long and winding road

I have been pointing out that the "birdlike cluster" is not related to the "tyrannosaur cluster". But the situation is actually more interesting than that.
In every cladogram that purports to show an evolution from dinosaur to bird, we find the following:
The dino-to-bird enthusiasts place non-flying creatures like the Ornithomimosauria, Therizinosauridae and Oviraptorosauria between the dinosaurs (eg. tyrannosaurs) and the birds.
The idea is that terrestrial dinosaurs evolved into terrestrial, feathered creatures which then evolved into flying birds.
But take a look at the Senter scatterplot. Trace the line that is imagined to have occurred between these groups, supposedly winding its way to the birdlike cluster.
It is a wandering line between groups that are not connected.
The dino-to-bird idea is completely incompatible with the evidence from the Senter study.

For those who might like to have this spelled out, the dino to bird purported sequence would roughly go from the red points to the pink points, backtrack to the olive points, over to the green points, over to the blue points and then backtrack to the violet points. Quite a fantastic, supposed journey.
When the data is accurately charted like this we see that the dino to bird idea is simply incorrect.

Thursday, August 26, 2010

The "birdlike cluster"

Senter has shown that there is a "birdlike cluster" which is "morphologically continuous". When we look at what creatures are included in the birdlike cluster, we see that they are all "maniraptors".
This is precisely one of the major points I have been making. The group labeled "maniraptors" are in fact flying and secondarily flightless birds. (Of course I am not the only one who has made this point).

I am also saying that the flying birds within the birdlike cluster developed from pterosaurs. And the flightless birds within the birdlike cluster developed from the flying birds within the birdlike cluster.

An intellectual exercise

Here is an intellectual exercise.
Let us take the 3 groups:
A: Non-maniraptor dinosaurs (eg Tyrannosaur, Compsognathidae)
B: Non-avian maniraptors (eg. Dromaeosaurids, Oviraptors etc.)
C: Aves (eg. Enantiornithes, Confuciusornis etc.)

People agree that C is related to B.
But some people go further and say also that B is related to A.
But the people who believe that B is related to A, do not put it in that simple way. They keep saying that C is related to the "non-avian group" (A + B).
To be precise, C is related to the B part of the "non-avian group", not the A part of the "non-avian group". The phrase "non-avian group" is just misleading. Whether B is related to A has still to be shown.
And that is the question!
Does everyone see the issue?

And then think about how many times you have seen the phrases "non-avian coelurosaurs" and "non-avian dinosaurs".

Tuesday, August 24, 2010

Trajectories

Here is what Senter says about "trajectories of dots" (morphological evolution within a lineage):
"It is noteworthy that bifurcating trajectories are visible in the 2009 scatter plot in a number of places. Within Dromaeosauridae, the sequence Velociraptor [dot 28]→Deinonychus [dot 29] and the sequence Sinornithosaurus [dot 26]→Microraptor [dot 27] extend in different directions from Bambiraptor, which is at the apex of the 'V'. Another bifurcation is present within the Tyrannosaur Cluster, with Guanlong + Ornitholestes at its apex and with Gorgosaurus→Tyrannosaurus leading in one direction and Huaxiagnathus→ (Sinosauropteryx + Compsognathus) leading in another direction. Baraminologists recognize that a trajectory of dots within a CMDS or ANOPA scatter plot represents morphological evolution within a lineage (Wood & Cavanaugh, 2003; Wood, 2005a,b), in which case bifurcating trajectories must represent speciation. It is also noteworthy that these bifurcating patterns correspond reasonably well to the bifurcations on the cladogram in Fig. 1, with the more basal members of each group closer to the origin of each scatter plot bifurcation."

As an example, let's focus on:
"Within Dromaeosauridae, the sequence Velociraptor→Deinonychus and the sequence Sinornithosaurus→Microraptor extend in different directions from Bambiraptor"

On the cluster diagram, he is referring to Velociraptor (dot 28) being close to Deinonychus (dot 29). And he is referring to Sinornithosaurus (dot 26) being close to Microraptor (dot 27). This all makes sense. As Senter says this "represents morphological evolution within a lineage".
BUT here is the big point. We do not see anything like this between the "Tyrannosaur cluster" and the "Birdlike cluster". These clusters are separate, with no trajectory of dots between them.
So by Senter's own logic, the "Birdlike cluster" is not related to the "Tyrannosaur cluster".
And even though Senter himself does not draw the obvious conclusion, the obvious conclusion is that birds did not develop from dinosaurs.

Monday, August 23, 2010

A matter of perspective

The Senter cluster diagram shows two different 3D perspectives on the 2009 same data. It can be confusing if one does not fully realize this. For example the chart on the right seems to show that the violet dots and the pink dots are close together. But of course they are not, as we can clearly see from the chart on the left. It is just an illusion of perspective. This is probably obvious to most every one but it may have confused a few people.

Analyzing the clusters

Let's see what more we can learn from the clusters.



First we can see that the dots cluster into well-known groups*.
Violet dots for Aves.
Dark blue for Dromaeosauridae.
Light blue for Troodontidae.
Red for Compsognathidae.
Pink for Tyrannosaurs.
Green (light and dark) for Oviraptors.

This gives credence to the placement of the dots.
But what is striking is that the clusters are separate from each other. There are no lines of intermediates.
And it is clear how Senter established the Birdlike cluster and the Tyrannosaur cluster. It is clear that they are separate.

*There are other groups than the ones I listed, but these are the ones of most interest.

Relating the Senter study

So how does the Senter study relate to the theory being presented in this site?
The Senter study shows that the Tyrannosaur cluster (Tyrannosaur, Compsognathidae etc) does not relate to the Birdlike cluster. This is strong support for the idea that birds did not develop from dinosaurs.
Now the Senter study was undertaken in an attempt to show that "creationists" need to accept the idea of evolution. However the study actually does the opposite. Creationists can take from the study support for their idea of created kinds.
That is a conclusion that can be made.
I am taking a less controversial position.
I am saying that birds developed from pterosaurs. The Senter study shows that birds did not develop from dinosaurs so the question of bird origins is still open.
A creationist could say that birds were a creation of a higher intelligence. I am saying that birds developed from pterosaurs.
What I am proposing is compatible with both evolutionism and creationism.

Why the Senter study is important

Why is the Senter (2010) study important?
For a few reasons.
1. The Senter study title and abstract are available online. (As is some of the supporting information). You have to pay to see the article itself. So most people will get their impression of the study only from what is available free online. This means that if the title and the abstract are misleading that is the only impression most people will get. As we have seen, the title and the abstract imply the opposite of what the study itself shows, so this is significant.
2. The Senter study uses CMDS which is not new in the baraminology literature but is not common in the mainstream evolution literature. Since this statistical technique is one more helpful tool, it is good that it has been referred to in the mainstream evolution literature.
3. Moving to the results of the study itself, we see that the Birdlike cluster and the Tyrannosaur cluster are separate, they are not related. This puts one more nail in the coffin of the dino to bird hypothesis.
4. Looking beyond just the subject of birds, Senter points out that:
"Using ANOPA and CMDS, baraminologists have conducted several searches for morphological gaps in extant and fossil taxa. Such studies have identified significant morphological gaps between major groups of extant and extinct cetaceans"
and
"Two such studies that included dozens of extant plant and animal taxa have verified that, in general, morphological gaps separate extant families from each other, but morphological continuity exists within families (Wood, 2005b, 2008a)."
So other currently assumed evolution lineages (not just birds) need to be re-considered.

Analyzing the title of the Senter study

Even the title of the Senter (2010) study is misleading.
Here is the title:
"Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs"

The first thing to notice is the identification of CMDS as a "creationist method". This is a bizarre thing to say, particularly when Senter himself says:
"It should be noted that ANOPA and CMDS are not strictly creationist techniques. They are mathematical techniques, and mathematics has no creed. "
So we can dismiss that misconception.

The second thing to note is that the title also implies that the study "demonstrates evolution", when in fact it demonstrates the independence of the Birdlike cluster and the Tyrannosaur cluster. In other words it demonstrates that birds are not related to coelurosarian dinosaurs (Tyrannosaurs, Compsognathidae etc).
So the title would be correct if it said something like:

"Using science to demonstrate independence: application of a statistical method for visualizing and quantifying gaps in the fossil record to a phylogenetic study of coelurosaurians."

Analyzing the Senter study abstract

Let's analyze the Senter (2010) study abstract and see why it is necessary to correct it. As it stands it is misleading.
Here is the corrected version:

It is important to demonstrate evolutionary principles in such a way that they cannot be countered by creation science. One such way is to use creation science itself to demonstrate evolutionary principles. Some creation scientists use classic multidimensional scaling (CMDS) to quantify and visualize morphological gaps or continuity between taxa, accepting gaps as evidence of independent creation and accepting continuity as evidence of genetic relatedness. Here, I apply CMDS to a phylogenetic analysis of coelurosaurian dinosaurs and show that it reveals morphological continuity between Archaeopteryx, other early birds, and a wide range of nonavian coelurosaurs MANIRAPTORS. Creation scientists who use CMDS must therefore accept that these animals are genetically related. Other uses of CMDS for evolutionary biologists include the identification of taxa with much missing evolutionary history and the tracing of the progressive filling of morphological gaps in the fossil record through successive years of discovery.

I have replaced the words "nonavian coelurosaurs" with the words "nonavian maniraptors".
Why is this important?
Well, the phrase "nonavian coelurosaurs" includes both "Birdlike cluster" creatures (eg. Confuciusornis, Sapeornis etc) and "Tyrannosaur cluster" creatures (eg Tyrannosaurs, Compsognathidae, etc).
But we see there is no connection between those groups. So it is misleading to imply there is "morphological continuity" between them. We need to distinguish between those groups and of course the phrase "nonavian coelurosaurians" does not make that distinction. In fact it hides it. By using the phrase "nonavian coelurosaurs" it makes it look as if there is "morphological continuity" between the Birdlike cluster and the Tyrannosaur cluster which there is not.
AND THAT IS THE ISSUE.

Note: "nonavian" is used by Senter and others to mean non-Aves.

Saturday, August 21, 2010

Clarifying the Senter study abstract

The Senter (2010) study abstract should actually say:

It is important to demonstrate evolutionary principles in such a way that they cannot be countered by creation science. One such way is to use creation science itself to demonstrate evolutionary principles. Some creation scientists use classic multidimensional scaling (CMDS) to quantify and visualize morphological gaps or continuity between taxa, accepting gaps as evidence of independent creation and accepting continuity as evidence of genetic relatedness. Here, I apply CMDS to a phylogenetic analysis of coelurosaurian dinosaurs and show that it reveals morphological continuity between Archaeopteryx, other early birds, and a wide range of nonavian coelurosaurs MANIRAPTORS. Creation scientists who use CMDS must therefore accept that these animals are genetically related. Other uses of CMDS for evolutionary biologists include the identification of taxa with much missing evolutionary history and the tracing of the progressive filling of morphological gaps in the fossil record through successive years of discovery.

Clusters

See link and download supporting Word document.
http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02039.x/suppinfo



Notice the "birdlike cluster" (dark blue, light blue and violet) and the separate "tyrannosaur cluster" (red, orange and
pink).
Note: The "birdlike cluster also contains taxa 14, 17 and 30 (see below).


-->
Table S10 Three-dimensional coordinates of the CMDS visualization of the 2009 matrix. Number and color on left refer to the label and color of each taxon’s point in the scatter plot (Figure 2). Note that closely related ingroups are given the same color, and non-coelurosaurian ougroups are black.
1 black                   Dilophosaurus      
2  black                  Allosaurus               
3 black                   Sinraptor                
4 pink                     Guanlong               
5 pink                     Gorgosaurus           
6 pink                     Tyrannosaurus        
7 red                       Sinosauropteryx     
8 red                       Huaxiagnathus       
9 red                       Compsognathus      
10 orange               Ornitholestes          
11 gold                   Gallimimus             
12 gold                   Ornithomimus         
13 gold                   Struthiomimus        
14 yellow Falcarius               
15 yellow Therizinosaurus
+ Segnosaurus
+ Erlikosaurus
+ Erliansaurus
+ Neimongosaurus                 
16 olive                   Shuvuuia                                
17 light green          Protarchaeopteryx


-->
+ Incisivosaurus  
18 light green          Caudipteryx           
19 dark green         Citipati                  
20 dark green         IGM 100/42           
21 dark green         Ingenia                   
22 dark green         Khaan                     
23 light blue            Anchiornis            
24 light blue            Mei                         
25 dark blue           Bambiraptor         
26 dark blue           Sinornithosaurus   
27 dark blue            Microraptor           
28 dark blue           Velociraptor          
29 dark blue           Deinonychus         
30 magenta             Epidendrosaurus
+ Epidexipteryx   
31 violet                  Archaeopteryx       
32 violet                  Sapeornis               
33 violet                  Confuciusornis      


http://onlinelibrary.wiley.com/enhanced/doi/10.1111/j.1420-9101.2010.02039.x/

The 2009 matrix (Fig. 2) reflects the new discoveries of several taxa that bridge gaps between formerly separated clusters. With the addition of the basal tyrannosauroid Guanlong and the basal compsognathids Huaxiagnathus, a coherent cluster (hereafter called the Tyrannosaur Cluster) is formed by Tyrannosauroidea, Compsognathidae and Ornitholestes. A second cluster, hereafter called the Birdlike Cluster, includes basal birds and the birdlike taxa Dromaeosauridae, Troodontidae, Epidendrosaurus + Epidexipteryx, [scansoriopterids] Protarchaeopteryx [oviraptor]Incisivosaurus [oviraptorand Falcarius [Therizinosaur]

Between the least-separated members of the two clusters (Guanlong in the Tyrannosaur Cluster and Falcarius in the Birdlike Cluster) is a gap of only 0.135, which is smaller than the span of either cluster (0.143 for the Tyrannosaur Cluster, and 0.263 for the Birdlike Cluster). Distances of ≥ 0.200, indicating gaps, continue to isolate Oviraptoridae, CaudipteryxShuvuuia, Ornithomimidae and Therizinosauridae from all other taxa.


Let's begin with a precise listing of which taxa are in the "Birdlike cluster" according to Senter:
Dromaeosauridae (dark blue): 25, 26, 27, 28, 29
Troodontidae (light blue): 23, 24
Aves (violet): 31, 32, 33
Protarchaeopteryx + Incisivosaurus (light green): 17
Epidendrosaurus + Epidexipteryx (magenta): 30 
And Senter says these are a morphologically continuous group. 

Turning to the "Tyrannosaur cluster", Senter includes:
Tyrannosauroidea (pink): 4, 5, 6
Compsognathidae (red): 7, 8, 9
Ornitholestes (orange): 10 
And Senter says these are a morphologically continuous group. 

Thursday, August 12, 2010

More studies - more evidence

Here is a very recently published study (Senter 2010):

"Using creation science to demonstrate evolution: application of a creationist method for visualizing gaps in the fossil record to a phylogenetic study of coelurosaurian dinosaurs"

Abstract:
http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02039.x/abstract

Supporting information:
http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02039.x/suppinfo

A careful read of this shows what we have seen as a definite pattern. There is great morphological evidence for a "Tyrannosaur cluster" and also for a "Bird-Like Cluster".
But no evidence that those two groups are related.

Here is the interesting way the article puts it:
"As shown here, according to one of their own statistical measures, baraminologists must consider Archaeopteryx and other basal birds – including the more typically birdlike Confuciusornis and Sapeornis– the genetic relatives of dromaeosaurids and other birdlike coelurosaurs, and possibly even compsognathid and tyrannosauroids."

It uses the word MUST in reference to the relatedness within the Bird-like cluster.
But it uses the word POSSIBLY for any relatedness between that group and compsognathid and tyrannosauroids. Which is where the actual issue is.

AND

"Tyrannosauroidea, Compsognathidae and Ornitholestes [the "Tyrannosaur cluster"] form a morphologically continuous group. Basal birds (Archaeopteryx, Confuciusornis, Sapeornis) are part of a morphologically continuous group that also includes Dromaeosauridae, Troodontidae, Epidendrosaurus + Epidexipteryx, Protarchaeopteryx + Incisivosaurus and Falcarius [the "Birdlike cluster"]. Therefore, baraminologists must consider the members of each group to be genetically related. The distance between the two groups is also small enough that within the baraminological paradigm both groups are arguably genetically related to each other."

Again the same story. There is great morphological evidence for a "Tyrannosaur cluster" and also for a "Bird-Like Cluster". But no evidence that those two groups are related.

Thursday, August 5, 2010

Up in the Air

If you think that things are nailed down concerning the basics of birds - think again!

http://en.wikipedia.org/wiki/Enantiornithes

Phylogeny

"Enantiornithes is the sister group to Ornithurae or Ornithuromorpha depending on the taxonomic authority, and together they could form a clade called Ornithothoraces. Most phylogenetic studies have recovered Enantiornithes as a monophyletic group distinct from the modern birds and their closest relatives. The 2002 phylogenetic analysis by Clarke and Norell, though, reduced the number of enantiornithine autapomorphies to just four.[2] This raises the possibility that the discovery of new fossils could unite Enantiornithes and the birds closer to living species into one clade. If this proves to be true, then Enantiornithes is a paraphyletic taxon and thus phylogenetically invalid. All enantiornithines would then be united in the next larger clade Ornithothoraces instead, and called "ornithothoracines". (see Apsaravis for more on the possible invalidation of Enantiornithes)

On the other hand, Confuciusornis might be closer to Enantiornithes than to living birds rather than about equally distinct from both, which in turn would render the Ornithothoraces meaningless too. In that case, the Pygostylia would apply, but that taxon, too, is ill-defined. Altogether, the radiation of the early truly avian lineages (as opposed to "dinobirds" like Archaeopteryx or Dalianraptor) presents a highly confusing picture at present, and while the apparent deep divergence between Enantiornithes and Neornithes seems real, the relationships of these two and other Cretaceous groups like Hesperornithes or Liaoningornithiformes is not well resolved."

"Enantiornithine systematics are also highly provisional. The version used here, although based on many sources, is only tentative, and in need of revision in light of abundant new fossil discoveries. What appears fairly certain by now[20] is that there were subdivisions within Enantiornithes possibly including some minor basal lineages in addition to the more apomorphic Euenantiornithes. The latter may be a clade or an evolutionary grade (and hence are also of questionable validity). The details of the interrelationship of all these lineages, indeed the validity of most, is disputed, although the Avisauridae, for one example, seem likely to constitute a valid group. Phylogenetic taxonomists have hitherto been very reluctant, and justifiably so, to suggest delimitations of enantiornithine clades.[21]"

AND

"A consensus of scientific analyses indicates that Enantiornithes is one of two major sister groups of derived birds. The other group is the Ornithurae, which includes all living birds as a subset. This means that Enantiornithines are a successful branch of bird evolution, but one that diversified entirely separately from the lineage leading to modern birds.[1] This consensus has never been universally accepted and is being challenged by new studies, so that it is possible that enantiornithines may actually represent successive outgroups on the lineage leading to modern birds.[2]"

Sunday, August 1, 2010

More on flying to flightless

It is interesting to analyze the dromaeosaurids and the troodontids.
Let's begin with the dromaeosaurids.
The dromaeosuarids fall into two groups. One group includes deinonychus, microraptor, graciliraptor and utahraptor etc. This group dates to around 125 mya. If we look at the characteristics of this group we find flying bird characteristics such as aerodynamic flight (asymmetric) feathers.
The other group of dromaeosuarids includes dromaeosaurus, saurornitholestes, bambiraptor, mahakala, unenlagia and velociraptor etc. This group dates to around 75 mya. In this second group we find flightless bird characteristics, such as only symmetric feathers.

And we find troodon and saurornithoides etc from around 75 mya with flightless bird characteristics.

The fossil record (even if incomplete) tells a clear story. Flying birds were from very early on, with flightless birds later (closer to today).