Monday, December 28, 2015

Euparaves (5)

From the previous post:
The most parsimonious alternative is that the basalmost Euparaves were feathered, long-bony-tailed, flying primitive birds. And the ground-dwelling oviraptors and alvarezsaurids that came later, were secondarily flightless.

Is this a problem for the dinosaur to bird theory?
Indeed it is.
It is a problem because the oviraptors and alvarezsaurids are considered to be outgroups (intermediates) between dinosaurs and Euparaves. But if oviraptors and alvarezsaurids are descended from flying Euparaves, then there is no lineage from dinosaurs to Euparaves.

Basal Euparaves were four-winged. The hindlimbs were feathered and acted as additional wings (hindwings). They contributed to lift and control.
This is important because they contributed to the ability of the basal Euparaves to fly.
Tetrapterygidae (meaning "four-wings") is a group of four-winged dinosaurs proposed by Sankar Chatterjee in the second edition of his book The Rise of Birds: 225 Million Years of Evolution, where he included Microraptor, Xiaotingia, Aurornis, and Anchiornis.[1] The group was named after the characteristically long flight feathers on the legs of all included species, as well as the theory that the evolution of bird flight may have gone through a four-winged (or "tetrapteryx") stage, first proposed by naturalist William Beebe in 1915.[2] Chatterjee suggested that all dinosaurs with four wings formed a natural group exclusive of other paravians, and that this family was the sister taxon to the group Avialae, although most phylogenetic analyses have placed the animals of his Tetrapterygidae elsewhere in Paraves, such as XiaotingiaAurornis, andAnchiornis being placed in Avialae.[3],d.dmo
The evolution of powered flight in birds remains a contentious issue in vertebrate paleontology. The diminutive predatory dinosaur Microraptor gui preserves evidence of extensive, lift-generating feathers on each manus and forearm, but also preserves evidence of lift-generating feathers associated with the hindlimbs, effectively forming a pair of “hindwings”.

Euparaves (4)

Notice that in the study below, Pedopenna is included with Epidexipteryx and Oviraptors within basal Euparaves. Other flying primitive birds such as Eosinopteryx, Aurornis, Xiaotingia and Anchiornis etc should also be included (with Pedopenna, Epidexipteryx and Oviraptors) as basal Euparaves. However, in this cladogram they are shown as troodontids. (They have been classified differently in various studies).

Let's now consider whether the basalmost Euparaves were ground-dwelling or whether they were flying in the trees. Pedopenna, Epidexipteryx and the other flying  primitive birds such as Eosinopteryx, Aurornis, Xiaotingia and Anchiornis etc were all flying in the trees.
So if the basalmost Euparaves were ground-dwelling, then they must all have BECOME flying primitive birds AFTER splitting from the dinosaur line. Not only that, but they must all have developed like that convergently, to become like the other flying birds that came later. That is not parsimonious. 

The most parsimonious alternative is that the basalmost Euparaves were feathered, long-bony-tailed, flying primitive birds. And the ground-dwelling oviraptors and alvarezsaurids that came later, were secondarily flightless.

For reference:
Pedopenna was originally classified as a paravian, the group of maniraptoran dinosaurs that includes both deinonychosaurs and avialans (the lineage including modern birds), but some scientists have classified it as a true avialan more closely related to modern birds than to deinonychosaurs.[3]

Thursday, December 24, 2015

Powered flight, flapping flight, gliding (2)

Basal Euparaves could fly by flapping their wings, but they lacked the muscle structure to take off from the ground. In other words, they could fly but they were not capable of "powered flight".
Some of the literature gives the impression that they could only glide and parachute. 
But they could fly. They just were not capable of "powered flight" (they could not take off from the ground).
And basal Euparaves could fly even though they did not have asymmetric feathers. 

This is all very important because the dinosaur to bird theory is built on the idea that basal Euparaves could not fly. 

Wednesday, December 23, 2015

Let's take a break


Powered flight, flapping flight, gliding

Basal Euparaves could fly by flapping their wings, but they could not take off from the ground. In other words, they capable of "powered flight" but not able to takeoff from the ground.
.... the work of Xu et al. (2003), (2005) and Hu et al. (2009) provide examples of basal and early paravians with four wings,[11][12][13] adapted to an arboreal lifestyle who would only lose their hindwings when some adapted to a life on the ground and when avialans evolved powered flight.[14] Newer research also indicates that gliding, flapping and parachuting was another ancestral trait of Paraves, while true powered flight only evolved once, in the lineage leading to modern birds.[15]

"Out of all these flappers and gliders, only the birds seem to have been capable of powered flight," said co-author Mike Benton, Professor of Vertebrate Palaeontology at Bristol.

The lack of a morphologically derived SC [supracoracoideus] in Late Jurassic and Early Cretaceous birds precluded a high velocity recovery stroke which undoubtedly limited powered flight in these forms. Subsequent evolution of the derived SC capable of imparting a large rotational force to the humerus about its longitudinal axis was an important step in the evolution of the wing upstroke and in the ability to supinate (circumflex) the manus in early upstroke, a movement fundamental to reducing air resistance during the recovery stroke.
Euavialae (meaning "true winged birds") is a group of birds which includes all avialan species more closely related to modern birds, than to the primitive, long-tailed birds Archaeopteryx and Jeholornis.[1]
The dorsal elevators, principally the deltoideus major, can effect the recovery stroke by themselves, as they did in Archaeopteryx. The German anatomist Maxheinz J. Sy proved this when he cut the tendons of the supracoracoideus in living crows and pigeons (1936). Sy found that pigeons were capable of normal, sustained flight; the only capacity they lost was the ability to take off from level ground.

Concerning flapping flight, also see:

Tuesday, December 22, 2015

Euparaves (3)

Notice that Pedopenna is included with Epidexipteryx as a basal Euparaves. Those are just two of the flying basal Euparaves*. (Brusatte et al, 2014)

* Here are other flying basal Euparaves:
Scansoriopterygids (Temporal range: Late Jurassic, 165–156 Ma)
Anchiornis (Temporal range: Late Jurassic, 161–160.5 Ma)
Aurornis (Temporal range: Late Jurassic, 160 Ma)
Xiaotingia (Temporal range: Late Jurassic, 160 Ma)
Pedopenna (Temporal range: Middle or Late Jurassic, 164 Ma)
Eosinopteryx? (Temporal range: Late Jurassic, 160 Ma)

Monday, December 21, 2015

Pterosaur and Basal Euparaves

Pterorhynchus (Rhamphorhynchidae)

Scansoriopteryx (Scansoriopterygidae)

Note that in cladistics terms, basal Euparaves did not evolve from Pterorhynchus, but rather they share a common ancestor.
In non-cladistic terms, we could say that basal Euparaves evolved from a creature like Pterorhynchus. We can see that that is credible, from the drawings above.

For reference:,d.dmo (O'Connor and Sullivan2014)

Fig. 7 Tails and pelves of derived maniraptoran theropods (modified from Persons et al., in press)
A. Anchiornis (Deinonychosauria: Troodontidae?); B. Archaeopteryx (Aves); C. Jeholornis (Aves); D. Confuciusornis (Aves); E. Gallus (Aves); F. Caudipteryx (Oviraptorosauria); G. Khaan (Oviraptorosauria); H. Epidendrosaurus (Scansoriopterygidae); I. Zhongornis (incertae sedis); J. Epidexipteryx (Scansoriopterygidae) Color key: blue short proximal caudal vertebrae; green transitional caudals; yellow elongate distal caudals; orange partially or fully fused terminal caudals (pygostyle)

Sunday, December 20, 2015

Euparaves (2)

This is a cladogram from an earlier post.
It shows the placement of Euparaves, but the cladogram is still not completely correct since Euparaves is not actually connected to dinosaurs.

Euparaves (node-based) definition:
"The most recent common ancestor of Epidendrosaurus ninchengensis (Scansoriopterygidae) and Passer domesticus (the house sparrow), and all descendants thereof".

Here is the stem-based definition of Euparaves:
"The most inclusive clade containing Passer domesticus (Linnaeus 1758) but not Pterorhynchus wellnhoferi."

Here are the apomorphies of Euparaves:
possessed remiges and rectrices, that is, enlarged, stiff-shafted, closed-vaned (= barbules bearing hooked distal pennulae), pennaceous feathers arising from the distal forelimbs and tail
possessed feathered wings used in flapping flight

Concerning flapping flight, also see:

Tuesday, December 15, 2015

Pyramid reduction hypothesis

The pyramid reduction hypothesis is a credible explanation of the origin of bird fingers. It is "developmentally plausible, and is also consistent with the phalangeal reduction pattern seen in basal birds."
It is consistent with a pterosaur to bird theory.
It is inconsistent with a dinosaur to bird theory.
(Xu and Mackem 2013)
The ‘pyramid reduction hypothesis’ assumes II-III-IV identities
for neornithine manual digits and postulates the existence
of a conservative five-digit pattern with a gradual,
bilateral reduction of phalanges and metacarpals in avian
evolution [9]. One proposed mechanism postulates that an
elevation in peripheral BMPs, signaling factors that modulate
cell survival and proliferation [60,61], drove bilateral medial
and lateral digital reduction [9]. This hypothesis is developmentally
plausible, and is also consistent with the phalangeal
reduction pattern seen in basal birds [9,23]. However, it predicts
that the direct avian ancestor had a five-fingered hand
with dominant digits II, III, and IV [9] which is inconsistent
with the digital reduction data from basal theropods (e.g.,
all known basal theropods, including ceratosaurs, have a
vestigial digit IV) [5,62–64].
In fact, the pyramid reduction hypothesis implies that either birds are not descended from theropod dinosaurs, or that some as yet to be discovered
basal theropods were five-fingered with dominant digits II, III, and IV.

And concerning the alternative homeotic shift (frameshift):
Also, it is difficult to identify plausible selective pressures that would drive this type of homeotic shift, considering that the post-frameshift adult hand would be morphologically identical to the pre-frameshift condition [69].
We report herein that a pentadactyl developmental pattern is evident in early wing morphogenesis of Gallus (chicken) and Struthio (ostrich). Five avascular zones (spatially predestined locations of contiguous metacarpal and phalangeal aggregation) and four interdigital vascular spaces are established by the regression patterns of autopodial vasculature. Transient vestiges of the first and fifth metacarpals are confirmed histologically and histochemically. They lie within the preaxial-most and postaxial-most avascular zones, respectively. These observations reveal conservative patterning of the avian hand and corroborate a II-III-IV metacarpal interpretation, argue for II-III-IV identity of ossified digits in birds, and favour a simple reduction rather than a homeotic shift in terms of the phenotype expressed by Hox genes in the phylogeny of the avian manus. We suggest that gradual, bilateral reduction of phalanges and metacarpals, via apoptosis mediated by BMP, occurred during the evolution of birds (Pyramid Reduction Hypothesis). This is congruent with the establishment of a central wing axis that became co-opted for coordinated movements. On the basis of evidence presented here, the direct avian ancestor is predicted to have been five-fingered with dominant digits (+ metacarpals) as follow: II, III, IV.

Note the following from Xu and Mackem 2013:
"However, it predicts that the direct avian ancestor had a five-fingered hand with dominant digits II, III, and IV [9], which is inconsistent with the digital reduction data from basal theropods (e.g., all known basal theropods, including ceratosaurs, have a vestigial digit IV) [5,62–64]."

Xu and Mackem note that the Pyramid Reduction Hypothesis "is inconsistent with the digital reduction data from basal theropods". But it is only inconsistent if birds evolved from dinosaurs. If birds did not evolve from dinosaurs, then there is no inconsistency. 
In fact, as Xu and Mackem acknowledge, one possible implication of the Pyramid Reduction Hypothesis is that "birds are not descended from theropod dinosaurs".

And here is an even more subtle point:
Xu and Machem conclude that for the Pyramid Reduction Hypothesis to be correct:
"the direct avian ancestor had a five-fingered hand with dominant digits II, III, and IV".
They have overlooked the possibility that the ancestor had digits I-II-III-IV and lost digit I in the transition to primitive bird. Which is what I suggest occurred in the transition from pterosaur to primitive bird.

For years, people have been striving to reconcile the I-II-III digits of dinosaurs with the II-III-IV digits of birds.
Because they believe that birds evolved from dinosaurs.
Why do they believe that?
Because the cladistic analyses seem to support that idea.
How so?
Because they show oviraptors and alvarezsaurs as intermediates (outgroups) between dinosaurs and primitive birds (Euparaves).
BUT recent studies show that oviraptors and alvarezsaurs are WITHIN Euparaves.
So there is no cladistic analysis evidence to support the dino to bird theory.
Therefore there is no reason to strive to reconcile the I-II-III digits of dinosaurs with the II-III-IV digits of birds.
Which is good, because there is no credible way to reconcile them in the first place.

For reference:
Reply to “Limusaurus and bird digit identity”
Xing Xu1, James Clark2, Jonah Choiniere2, David Hone1 & Corwin Sullivan1
Morphological data from extinct theropods, even without considering Limusaurus and ceratosaurs, clearly contains two contradictory signals for the identification of tetanuran manual digits. Thus, neither our hypothesis nor the frameshift hypothesis is able to avoid a substantial number of homoplasies.

Sunday, December 13, 2015

Oviraptors and Alvarezsaurids within Euparaves

In the previous post, we saw analyses from 2009, 2011, 2013, 2014 and 2015 that show oviraptors and/or alvarezsaurids to be within Euparaves. (In other words, within the clade based on the common ancestor of Epidendrosaurus and Gallus).

What are the basalmost taxa within Euparaves? They are the Scansoriopterygidae, Anchiornis, Aurornis, Xiaotingia and Pedopenna. They are flying, arboreal, primitive birds.

On the other hand, Oviraptors and Alvarezsaurids were ground-based. They were secondarily flightless, as some previous analyses have found.

What is the significance of this? It means that Oviraptors and Alvarezsaurids are not intermediate (not outgroups) between dinosaurs and flying primitive birds.
That is like having the foundation of the dino to bird theory kicked out. There is no connection between dinosaurs and primitive birds.

As a sidenote, keep in mind also that Eudromaeosaurids are secondarily flightless, primitive birds within Euparaves. They are not intermediate (not outgroups) between dinosaurs and flying primitive birds.

Friday, December 11, 2015

Different placements of oviraptors and alvarezsaurids

Here are cladograms with oviraptors and/or alvarezsaurids within Euparaves. (Cau et al 2015)
Oviraptors within Euparaves.
Updated dataset of Brusatte et al. (2014).

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Object name is peerj-03-1032-g005.jpg

Cladogram based on a subset of taxa from Xu et al 2009 study:
Both Alvarezsaurids and Oviraptors within Euparaves.
For details see here.

Cladogram based on all data except Epidexipteryx from Xu et al 2009 study.
Both Alvarezsaurids and Oviraptors within Euparaves. (2009)
Figure S7 of the Xu et al 2009 study using ALL taxa:
Alvarezsaurids within Euparaves. Angolin and Novas (2011)  Figure 1(B)
Alvarezsaurids within Euparaves

From Agnolín and Novas  (2013):
Agnolín and Novas (2013) recovered scansoriopterygids as non-paravian maniraptorans and the sister group to Oviraptorosauria.[11] (Brusatte et al 2014)
Oviraptors within Euparaves. (Also see Figure S2 for more details.)
Notice that Pedopenna is included with Epidexipteryx within Euparaves.,d.dmo (O'Connor and Sullivan 2014)
Zhongornis and Oviraptors within Euparaves.

Thursday, December 10, 2015


In order to talk about the origin of primitive birds it is necessary to introduce a new clade name, Euparaves.
Euparaves (node-based) definition:
"The most recent common ancestor of Epidendrosaurus ninchengensis (Scansoriopterygidae) and Passer domesticus (the house sparrow), and all descendants thereof".

Here is the stem-based definition of Euparaves:
"The most inclusive clade containing Passer domesticus (Linnaeus 1758) but not Pterorhynchus wellnhoferi."

Here is the apomorphy-based definition of Euparaves:
possessed remiges and rectrices, that is, enlarged, stiff-shafted, closed-vaned (= barbules bearing hooked distal pennulae), pennaceous feathers arising from the distal forelimbs and tail
possessed feathered wings used in flapping flight

Alvarezsaurids and oviraptors are taxa within Euparaves. They are secondarily flightless, primitive birds that descended from flying basal Euparaves.

Here is a sample of flying, basal Euparavians:
Scansoriopterygids (Temporal range: Late Jurassic, 165–156 Ma)
Anchiornis (Temporal range: Late Jurassic, 161–160.5 Ma)
Aurornis (Temporal range: Late Jurassic, 160 Ma)
Xiaotingia (Temporal range: Late Jurassic, 160 Ma)
Pedopenna (Temporal range: Middle or Late Jurassic, 164 Ma)

These require further analysis:
Eosinopteryx? (Temporal range: Late Jurassic, 160 Ma)
Zhongornis? (Temporal range: Early Cretaceous, 122 Ma)

Oviraptors, Alvarezsaurids and Eudromaeosaurids are secondarily flightless, primitive birds within Euparaves.

Wednesday, December 9, 2015

"Indistinguishable from random"

Here is a study on how the published dinosaur cladograms compare to the stratigraphic (time) record. It is significant that there is a total lack of congruence, it is "indistinguishable from random", for Paraves.

Wills et al (2008): (Full article) (Table 1)
Evidence for the evolutionary history of most groups derives from two independent sources. The first is the distribution of phylogenetically informative characters or markers in extant and extinct taxa. The second is the stratigraphic or temporal sequence in which taxa occur as fossils. Neither source of data can be read uncritically, and both require interpretation. Phylogenies incorporate assumptions concerning rooting and models of evolution. The resulting trees are therefore inferences rather than data. Fossils require varying degrees of interpretation depending upon the nature of the material, and dates may be subject to large margins of error. For these reasons, it is often desirable to compare inferences by mapping cladograms onto stratigraphic range charts
"Over all 19 data sets, congruence was extremely high (Table 1). The average GER (Wills, 1999) for static first occurrence dates was 0.767, with the best data set being the Hadrosauridae (Horner et al., 2004; 0.956) and the worst being the Paraves (Turner et al., 2007; 0.558)."

" The least congruent data sets were the Paraves (Turner et al., 2007; GERt = 0.571), Stegosauria (Galton and Upchurch, 2004b; GERt = 0.611), Prosauropoda (Galton and Upchurch, 2004a; GERt = 0.720), and Ceratopsia (Xu et al., 2002; GERt = 0.755)."

Paraves is objectively calculated as the worst in terms of congruence. In fact, the article says that it is "indistinguishable from random". And that is because it is based on the incorrect dino-to-bird idea.

This is even worse when you consider the high congruence of dinosaurs in general:
Preliminary reanalysis of the 1,000 animal and plant “static” data sets utilized by Benton et al. (2000) and Wills (2007) yielded an average GER* of 0.688, with only 34% attaining a GER* > 0.975. This strongly suggests that the congruence of dinosaur phylogenies is better than that for a large sample of data sets across a range of other taxa.

Monday, November 16, 2015

The bigger picture

Here is the bigger picture.
We can see the dinosaur branch that simply went extinct, and the pterosaur branch that leads to birds.

Here is a cladistic analysis, which confirms the placement of Oviraptors (eg. Hagryphus, Conchoraptor) and Alvarezsaurids (eg. Mononykus, Shuvuuia) within Paraves:

Here is the TNT input file, which is based on the data from:

A Jurassic ceratosaur from China helps clarify avian digital homologies (2009)

517 17

Euparkeria ???0000?0?000???00?0?00000000000000000001??00000000000?0?1000??0


Allosaurus ???0?0100101?0000?000?10?010?0??0??0????11??00000111?0??11001000?


Tyrannosaurus ???100000011101011101100000000001110010?00221000001110??1111010





Gallus 0








Important note (not directly related to the above): 
Be aware that [cladistic analysis] programs can give different answers (trees) depending on the order in which the sequences appear in the input file. PHYLIP, PAUP and other phylogenetic software provide a ‘‘jumble’’ option that reruns the analysis with different (jumbled) input orders. If for whatever reason the tree must be computed in a single run, sequences that are suspected of being‘‘problematic’’ should be placed toward the end of the input file, to lower the probability that tree rearrangement methods will be negatively influenced by a poor initial topology stemming from any problematic sequences.

Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different "best" cladograms. In these situations, the user should input the data in various orders and compare the results.
Using different algorithms on a single data set can sometimes yield different "best" cladograms, because each algorithm may have a unique definition of what is "best".
Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A nonoptimal cladogram will be selected if the program settles on a local minimum rather than the desired global minimum.[14] To help solve this problem, many cladogram algorithms use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one.[15]

Saturday, November 14, 2015


The dino to bird theory requires "remarkable" reversals. 

ANKLE: (2015)
The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the ‘ascending process’ (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin–disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution.
Also see here:
More remarkably, however, this finding reveals an unexpected evolutionary transformation in birds. In embryos of the landegg-laying animals, the amniotes (which include crocodilians, lizards, turtles, and mammals, who secondarily evolved live birth) the intermedium fuses to the anklebone shortly after it forms, disappearing as a separate element. This does not occur in the bird ankle, which develops more like their very distant relatives that still lay their eggs in water, the amphibians. Since birds clearly belong within landegg-laying animals, their ankles have somehow resurrected a long-lost developmental pathway, still retained in the amphibians of today -- a surprising case of evolutionary reversal.
We confirm the proximal–posterior bone is a pisiform in terms of embryonic position and its development as a sesamoid associated to a tendon. However, the pisiform is absent in bird-like dinosaurs, which are known from several articulated specimens. The combined data provide compelling evidence of a remarkable evolutionary reversal: A large, ossified pisiform re-evolved in the lineage leading to birds, after a period in which it was either absent, nonossified, or very small, consistently escaping fossil preservation.
Based on this study, the most parsimonious alignment is for the four digits of ceratosaurs to be I-II-III-IV and the three (and sometimes four) digits of all Tetanurae to be II-III-IV(V). Accepting such a topological shift at the base of Tetanura requires that the positional homology of the three digits of tetanurans is II-III-IV(-V), as suggested by Wagner and Gauthier34. Because the four digits of ceratosaurs are therefore most parsimoniously interpreted as I-II-III-IV, the small lateral metacarpal ossification of Guanlong35, Sinraptor36, and Coelurus represents the re-ossification of metacarpal V after it is lost at the base of Ceratosauria. The poor phylogenetic resolution for basal tetanurans in our study precludes us from hypothesizing whether this re-ossification event occurred once or more than once in the evolution of Theropoda. Likewise, the fourth metacarpal, which is reduced in primitive theropods and bears an unknown number of phalanges in Ceratosauria, re-acquires at least three phalanges in Tetanurans.

This implies the reduction of digit I before the divergence of the Ceratosauria and the
Tetanurae, the appearance of some polleciform features in digit II and the acquisition of a novel phalangeal formula (X-2-3-4-X) early in tetanuran evolution. Both modifications are partially indicated by the manual morphologies of ceratosaurs and more basal theropods. Also, they are indirectly supported by observations in living animals that a digit will display features normally associated with the neighbouring medial digit if the latter fails to chondrify in early development21, that phalangeal counts can vary even within species29, 42 and that secondarily cartilaginous elements can regain their ability to ossify43.

If BDR [Bilateral Digit Reduction] applies to the more inclusive Averostra, as the II-III-IV hypothesis suggests, early stages of tetanuran evolution must have involved loss of the already highly reduced metacarpal I, reduction in the length of metacarpal II, and the reappearance of additional phalanges on metacarpal IV. Both the I-II-III and II-III-IV hypotheses can claim a degree of support from morphological data, but the II-III-IV hypothesis is more parsimonious when developmental data from extant birds are considered.

There is no actual evidence for these reversals. The dino to bird theorists need to imagine they happened so the dino to bird theory does not collapse.

Monday, November 2, 2015

Unjustifiable assumptions of homology
Unjustifiable assumptions of homology incorporated
into data matrices.—The most glaring example of
this problem is the coding of avian and theropod
manual, carpal, and tarsal characters as if they were homologous, despite the ambiguity of the data, and despite the assumption this coding entails that
the BMT [birds are maniraptor theropods] hypothesis is correct a priori. 
Because of the above ambiguities, these five
sets of characters [the palate, the basipterygoid process, the carpus, the manus, and the tarsus] cannot be coded for birds and theropods without unjustified assumptions of
homology. They were not included in the primary
analysis of our matrix. This decision is
understood to be especially controversial, so
we have documented our reasoning, which was
based on careful review of the anatomical evidence,
in Appendix 3.

Criticisms of the James and Pourtless study:,d.cWw

James and Pourtless excluded the characteristics that are in dispute. That is impartial.
The critics object to that. The critics want things scored their way.