Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds
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- State Key Laboratory of Medical Genetics; Xiangya Medical School, Central South University
This manuscript is a preprint. A published version is available at:
http://tilgher.it/chrCorrelati/upload/doc/RB_Att_biolog.pdf (Peer Reviewed) Published after peer review. Citation: Huang, S. (2009) Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds. Rivista di Biologia / Biology Forum, 102: 20-22.- Document Type:
- Manuscript
- Date:
- Received 15 May 2009 19:03 UTC; Posted 27 May 2009
- Subjects:
- Bioinformatics, Evolutionary Biology
- Abstract:
Molecular analysis of collagen sequences from an 80 million year old hadrosaur B. canadensis and a 68 million year old dinosaur T. rex 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.
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2 comments
Since you brought up the topic of cherry picking, let us have a few general words on it first.
It is no surprise to anyone that selective presentation and misrepresentation by ignoring/overlooking the inconvenient frequently characterize the literature of evolutionary biology like no other branch of science. Despite his insistence that the Darwinian theory is completely true as in his latest book Why Evolution Is True, the leading evolution biologist Jerry Coyne had openly admitted this: “In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics.” Could anyone have any confidence on the words or beliefs of a practioner of the likes of phrenology?
Selective presentation is a form of pseudoscientific and self-deceiving practise but is unfortunately unavoidable in the past 150 years because the theoretical paradigm for evolution study is at best incomplete or merely Okay for microevolution but definitely mistaken for macroevolution. No one has in his right mind ever claimed, including Darwin himself or his latest worshipers the likes of Jerry Coyne and Richard Dawkins, that the existing theory has no contradictions. Naturally then, if you cannot make sense of all relevant data with your theory that is like a religion to you (which means you will never give it up no matter what the evidence says or how many contradictions), of course the only thing you can do is to account for a fraction of the data while cross your fingers that no one will notice the other data or that no one can verify your account because a test would take a few million years to perform. So, it is quite common to see a typical member of the current cohort of evolution researchers to do cherry picking in presenting a story or do the other side of the same coin, as you did here, in criticizing a coherent true story by picking on only 1% of the story while ignoring the other 99%.
I have repeatedly made this point in my recent papers: it is time to transform evolutionary biology from the likes of phrenology to the status of genuine science, which means that its theory must be held by the same minimum standard as any science, i.e., it must be internally coherent, must account for all relevant facts, and must not allow a single contradiction. Selective presentation or cherry picking or misrepresentation must be stopped for good. If you cannot do experiments that must take a million years to perform, the least you can do is to tell a coherent story with the facts that you have already got, with no contradiction allowed and every fact accounted for. While that is really a minimum standard for any kind of science, it has to be especially held as a must for macroevolution precisely because it is not accessible to direct experimental test, which makes it so much easier for people to freely offer wild ad hoc explanations with total disregard to the internal coherence of the whole and without any fear of ever being caught or proven incorrect. Other than a coherent story, we have no other way of knowing if you have complete truth. Other than an incoherent story, we have no other way of knowing if you only have incomplete truth. Macroevolution should be a branch of science that is most like mathematics given that neither is accessible to experimental test: the only and best proof of its theory is logical and factual coherence without a single contradiction.
I have no patience with such typical self-serving and self-deceiving claims that you don’t expect a theory of evolution to have no contradictions since most things are chance. The one thing that all genuine science like mathematics and physics have taught us is that it would take a miracle for an incomplete theory to have no contradictions and it would equally take a miracle for a complete theory to encounter a single contradiction in nature. The difference between truth and falsehood is not quantitative or measured by the difference in the number of contradictions but is qualitative.
Having openly made that point and subjected my own theory the MGD hypothesis to the same minimum standard of science as I am demanding of others, you would expect me to be the last person to commit the sin of selective presentation or hiding/ignoring contradiction. And, fact is, I view my life too short to waste time on non-productive and meaningless activities, like knowingly (or unknowingly due to incompetence) perpetuating falsehood or incomplete truth as the complete.
The meat of my paper or 99% of the story, which you have somehow managed to completely ignore in forming your opinion, is about the conserved nature of the amino acid position that is found different between the 80 million year old Hadrosaur and all the living and extinct amniotes that are younger than 68 million years for which we have sequence information (15 species in total). The conserved nature is such that if we see a living amniote with a Pro at this position (as we did with the Hadrosaur) rather than Ile (as we did with all informative living and extinct amniotes younger than 68 million years), we can be almost certain that there must be a sequencing error or that this amniote must be from another planet or a different era. If this position is not so remarkably conserved, no one in his right mind would have made anything out of it. On the other hand, it could only be characterized as gross incompetence in ignoring the significance of a change to such an extremely conserved position and in failing to see it as the key rationale for placing Hadrosaur as an outgroup to the T. rex-birds clade. Just like all birds have a terrestrially adapted egg, all birds including its closest fossil relative T. rex have Ile at this position. Of course I only have data for three living birds but I can nonetheless jusitify such a bold claim from the fact that this Ile is conserved between birds and mammals despite 300 million years of seperation, while seperation within birds is at most 65 million years.
How could you ever argue that ‘the Ostrich is basal to the chicken-dinosaur clade based on the additional amino acid difference (see table 1)’ when that amino acid position of concern is not even conserved between mouse and rat that have merely separated for 11 million years (see table 1)?
By the way, the paper is now in press after peer review.
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- This document is licensed to the public under the Creative Commons Attribution 3.0 License
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Huang, Shi. Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3255.1> (2009)
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Published version:
http://tilgher.it/chrCorrelati/upload/doc/RB_Att_biolog.pdf (Peer Reviewed) Published after peer review. Citation: Huang, S. (2009) Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds. Rivista di Biologia / Biology Forum, 102: 20-22. -
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Kim van der Linde on 18 June 2009 02:44 UTC
Interesting article, but unfortunately, it contains a potential methodological error that invalidates the result.
Using the same rational as for the chicken/hadrosaur/T.rex triplet, one could argue that the Ostrich is basal to the chicken-dinosaur clade based on the additional amino acid difference (see table 1). The logical implication of that argument would be that Paleognathae and Neognathae are two separate branches and that Aves as currently defined is paraphyletic. The article of Schweitzer et al leaves that possibility open, as the support for a monophyletic Aves clade is very low in both the Bayesian and Maximum likelihood analysis.
To me, this article feels like cherry picking some results that are in line with the preferred outcome, namely that birds are theropod dinosaurs, which requires that the Hadrosaur is placed basal to the Maniropteran clade.