Friday, May 15, 2009

Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds

Molecular analysis of collagen sequences from an 80 million year old hadrosaur B. canadensis and a 68 million year old dinosaur T. rex suggest that the two dinosaurs belong to a clade to the exclusion of birds [1,2,3].  However, well-established morphological analyses of fossils show that T. rex is more closely related to birds than it is to the ornithischian hadrosaur B. canadensis [4].  The molecular analyses were based on the molecular clock paradigm, which is known to be contradicted by fossil sequences [5,6].  It is therefore necessary to reevaluate the molecular data independent of the molecular clock paradigm. 

Here, I analyzed all the collagen sequences reported for B. canadensis and T. rex.  There are a total of four peptides whose sequences are known in the two dinosaurs and extant chicken.  But, only one of these is informative as the other three are identical among the three species.  For this single informative 18 amino acid peptide (GLPGESGAVGPAGPPGSR), I compared its sequence from all extant species including birds, reptiles, amphibians, fishes, and mammals where the sequence information is available (Table 1).  The data show that T. rex is identical to G. gallus whereas B. canadensis differs from T. rex and G. gallus at residue position 15.  An Ile residue at this position is completely conserved in all extant species of mammals, birds, and reptiles.  And yet, B. canadensis has a Pro at this position.  From the Dayhoff’s PAM (accepted point mutation) matrix [7], a change from Ile to Pro or vice versa is highly uncommon.  Furthermore, not a single extant species from mammals, birds, reptiles, amphibians, and fishes (19 species analyzed) has a Pro at this position.

These molecular data therefore suggest strongly that B. canadensis is an outgroup to a clade containing T. rex and birds, fully consistent with the well-established phylogeny based on morphological analyses of fossils [4].  The unusual change from a conserved Ile to a Pro also show that B. canadensis is genetically more distant to the outgroup fish than extant birds and reptiles, confirming the previous observation that ancient fossil specimens of extinct species are more distant to a simpler outgroup than extant sister species [5,6].  Thus, fossil sequences consistently contradict the molecular clock paradigm and would inevitably lead to absurd conclusions if analyzed under the assumptions of that paradigm.  


1. Schweitzer MH, Zheng W, Organ CL, Avci R, Suo Z, et al. (2009) Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324: 626-631.

2. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007) Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science 316: 280-285.

3. Asara JM, Schweitzer MH (2008) Response to Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 319: 33.

4. Pisani D, Yates AM, Langer MC, Benton MJ (2002) A genus-level supertree of the Dinosauria. Proc Biol Sci 269: 915-921.

5. Huang S (2008) Ancient fossil specimens are genetically more distant to an outgroup than extant sister species are. Riv Biol 101: 93-108.

6. Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, et al. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134: 416-426.

7. Dayhoff MO (1978) Atlas of protein sequence and structure. Washington, D.C.: National Biomedical Research Foundation.

Table 1. Sequence alignment of a peptide from collagen alpha 2 type 1.


B. Canadensis         GLPGESGAVGPAGPPGSR


T. rex                ..............I...

G. gallus             ..............I...

T. guttata            .P............I...

S. camelus            .P............I...


A. mississippiensis   ...........V..I...

A. carolinensis       .A.........S..I...


H. sapiens            .P......A..T..I...

M. mulluta            .P......A..T..I...

B. taurus             .P......A..T..I...

M. americanum         .P..Q...A..T..I...

L. afiricana          .P..Q...A..T..I...

M. musculus           .T......A..S..I...

R. norvegicus         .P......A..S..I...

E. telfairi           .P..Q...A..T.SI...


M. domestica          .P.........T.SI...


X. levis              .T......A..F..L.P.

X. tropicalis         .A......A..L.AL.P.

R. catesbeiana        .A.....GA..H.PS...


D. rerio              .N..PA..A.AQ..I.A.

O. mykiss             .NS.PA.SA.SQ.AI.A.

P. olivaceus          .IN.VA..S.VQ.AV.A.


Thursday, May 14, 2009

Some Darwinists do admit that the theory of natural selection is poorly supported

I have written a review ( of Jerry Coyne’s book ‘Why evolution is true’ and criticized the author for not distinguishing between the facts of evolution and the Darwinian theory of natural selection.  The facts are true but the theory is far from true as it has countless contradictions, which means that it is actually false, at least in its major claims on macroevolution.  This is such an obvious point that any competent intellectuals should be able to see.  Indeed, in a recent book review article (, the leading Darwinist Richard Lewontin of Harvard made a similar point.  Below is the relevant section from his review.

Where he (Coyne) is less successful, as all other commentators have been, is in his insistence that the evidence for natural selection as the driving force of evolution is of the same inferential strength as the evidence that evolution has occurred. So, for example, he gives the game away by writing that when we examine a sequence of changes in the fossil record, we can

“determine whether the sequences of changes at least conform to a step-by-step adaptive process. And in every case, we can find at least a feasible Darwinian explanation.”

But to say that some example is not falsification of a theory because we can always "find" (invent) a feasible explanation says more about the flexibility of the theory and the ingenuity of its supporters than it says about physical nature. Indeed in his later discussion of theories of behavioral evolution he becomes appropriately skeptical when he writes that

“imaginative reconstructions of how things might have evolved are not science; they are stories.”

While this is a perfectly good argument against those who claim that there are things that are so complex that evolutionary biology cannot explain them, it allows evolutionary "theory" to fall back into the category of being reasonable but not an incontrovertible material fact.

There is, of course, nothing that Coyne can do about the situation. There are different modes of "knowing," and we "know" that evolution has, in fact, occurred in a stronger sense than we "know" that some sequence of evolutionary change has been the result of natural selection. Despite these misgivings, it is the case that Coyne's book is the best general explication of evolution that I know of and deserves its success as a best seller

Monday, May 11, 2009

On the collagen sequence of the Campanian hadrosaurs (duck-billed dinosaur) B. Canadensis

Collagen sequences from an 80 million year old dinosaur were published recently. 

Schweitzer et al., 2009, Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. Canadensis, Science, 5927, pp. 626 - 631

Below I analyzed the 8 peptide sequences reported.  My analysis showed that B. Canadensis is an outgroup to a T.rex-bird clade, consistent with morphological data but different from the conclusion of Schweitzer et al.  Also, the analysis confirmed the major findings of my early fossil sequence paper.   



100% identical to mouse




100% T. rex, 100% chicken, and 100% mammals, 17/17, 100% mammut




100% T. rex, 100% chicken, 100% rana. 18/18, 17/18 homo, 17/18 mammut




100% Chicken, 17/18 rana, 17/18 homo, 16/18 mus, 13/18 match in mammut,




100% T. rex, 100% chicken, 100% frog/newt/rana, 17/18 homo, 17/18 mammut




100% Chicken, 100% rat, and 100% opossum. 14/15 mus, 13/15 homo, 12/15 mammut




Collagen a2(1)

100% Chicken, and 17/18 Taeniopygia guttata, 15/18, homo, 13/18 mammut




Collagen a2(1)

17/18 T. rex, 17/18 chicken, 16/18, Taeniopygia, 17/18 between chicken and Taeniopygia.  Much less to others.  18/18 between chicken and T. rex. 


Some questions:


1.  Is B. canadensis more related to T. rex than chicken is? 

No.  It is equidistant to chicken and T. rex.  And chicken is closer to T. rex than Bc is to T. rex.  The informative peptide in this case is #8.  Of 4 peptides whose sequences are known in Bc, Tr, and chicken, three (peptide #2, #3, #5) are non informative as they are identical among the three species.


2.  Is B. canadensis more related to birds than to other animals? 

Yes, informative peptides 4, 7, 8 show B. canadensis more similar to chicken than to frog or mammals or any other. 


3.  Is B. canadensis more related to bird than T. rex is?

The only informative peptide is #8.  For this peptide, Tr is 18/18 to chicken and 17/18 to Tg (Taeniopygia guttata).  Bc is 17/18 to chicken, and 16/18 to Taeniopygia.  So, Tr is more related to birds than Bc is.


4.  Is B. canadensis more distant to the outgroup frog than bird/mammal are?

Not a single informative peptide.   Seven of the 8 peptides are not unique to Bc.  Peptide 8 is unique but not very conserved in extant animals.


5.  Is the distance between B. canadensis and mammut greater than that between extant birds and extant mammals?

Yes.  Of 6 informative peptides (1-6 of collagen A1t1), 4 and 6 show that distance between Bc and mammut (25/33) is greater than that between birds and mammals (29/33).  The distance between extant birds and mammut is also greater than between extant birds and extant mammals.  This result confirms the previous finding on the distance between Tr and mammuts. Only the MGD but not the molecular clock hypothesis can predict such result.

Conclusion: Bc is the outgroup to a Tr-bird clade

Schweitzer et al stated: “However, on the basis of well-established morphological analyses (25), we predict that T. rex is more closely related to birds than it is to the ornithischian hadrosaur B. canadensis.” 25. D. Pisani et al., Proc. R. Soc. London Ser. B Biol. Sci. 269, 915 (2002).

Yet their molecular analysis based on certain statistical methods suggest that the two dinosaurs belong to a clade to the exclusion of birds.  Such a conclusion is false because it is based on the completely mistaken paradigm of molecular clock and neutral theory.  So, my analysis shows Bc as the outgroup to a clade containing birds and Tr.  This conclusion is more consistent with morphological analysis.  The fact that Tr is closer to a bird Gg than a bird Gg is to another bird Tg may be due to the fact that Tr has 60 million years less time to mutate than extant birds are, or that Tg had a different dinosaur ancestor.  

Thursday, May 7, 2009

A more accurate rendering of Table 1 in the MGD paper

The following modification of Table 1 of the MGD paper take into account those positions that are shared between species due to common adaptation to a common environmental selection, depicted by ‘#’.   Variant positions are denoted by 'x'. This more realistic rendering explains both equidistance and overlap features. It explains why not all variants between Hs and Dm are also variants between Hs and Sc or between Nc and Sc. Also see the related post on May 1, 2009 titled 'more on the MGD interpretation of certain facts.'

Table 1. Alignment of a hypothetical 20 amino acid peptide.

Nc     1 2 3 4 5 6 7 8 # 1 x 3 4 # x # x # x x     N. crassa

Sc     1 2 3 4 5 6 7 8 # 1 2 x x # x # # # x x     S. cerevisiae

Dm     1 2 3 4 5 6 7 8 # 1 2 3 4 5 6 # # x x x     D. melanogaster

Hs     1 2 3 4 5 6 7 8 # 1 2 3 4 # 6 7 # 9 9 x     H. sapiens

Equidistance feature:


Nc-Sc, 65% (13/20)

Dm-Sc, 65%

Dm-Nc, 65%

Hs-Sc, 65%

Hs-Nc, 65%

Hs-Dm, 75%

Overlap feature:

Of 5 variants between Hs-Dm, four are variants between Hs-Sc.

Of 5 variants between Hs-Dm, four are variants between Hs-Nc.

Of 5 variants between Hs-Dm, two are variants between Sc-Nc.  

Actual alignment of the above four species for cytochrome c:






                 *   **   *   * **** * **  * ** ***  **  *   *  ** ** 







                *   * *    *** *********** * * **   * * *   * **  


The existence of shared residues due to environmental selection is key to the adaptive survival of species over long evolutionary time.  The MGD predicts that while a simple organism may have great genetic diversity potential, only a fraction of the diversity is expressed at any one time due to natural selection to be the most optimal.  This view is fully consistent with one of the two most remarkable early results of molecular evolution: the levels of allozyme diversity vary by no more than a few fold across almost all species.  (the other result is of course the seemingly similar mutation rates in different species.)  This view is also fully supported by the work Eviatar Nevo on the ‘evolution canyon’ in Israel.

Nevo: “Natural selection in some form proved to be the major determinant of genetic population structure and differentiation. The parallel genetic patterns obtained across all geographical scales in nature were once again inconsistent with the neutral theory of molecular evolution.  Natural selection in its various forms appears to maintain genetic polymorphism and orient molecular evolution at both the protein and DNA level, as was also supported theoretically.”

Nevo E, Beiles A, Ben-Shlomo R (1984) The evolutionary significance of genetic diversity: ecological, demographic and life histroy correlates. In: Mani GS, editor. Evolutionary Dynamics of Genetic Diversity. Berlin: Spinger-Verlag. pp. 13–213.

Nevo E (2001) Evolution of genome-phenome diversity under environmental stress. Proc Natl Acad Sci U S A 98: 6233-6240.


I thank my college classmate Dr. Wei Shen for providing the actual sequence alignment shown here and for the helpful discussion on Table 1 of the MGD paper.