April 26, 2008 | David F. Coppedge

Inferences from Old Protein

The dinosaur leg bone with the soft tissue was back in the news.  Back in 2005 (03/24/2005), a femur from a T. rex broke open during transport and was found to contain pliable tissue and blood vessels with apparent red blood cells.  This was a “phenomenon, once thought impossible” for such tissues to have survived for 68 million years.  In 2007, the team of Mary Schweitzer announced the presence of collagen in the dinosaur and in a mastodon bone (04/12/2007).  A short update on the story was printed in Science.1  This paper said nothing about the sensation of finding soft tissue in old fossils.  The focus was almost entirely on evolution.
    The team from North Carolina State, Harvard and other institutions sequenced the collagen from both the dinosaur and the mastodon.  Finding evolution was their goal: “It was clearly the purpose of the research: “We performed phylogenetic analyses to infer the evolutionary relationships” of the dinosaur and mammal.  “Despite missing sequence data,” they said, “the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex..”  They concluded that “molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.
    The original paper only admitted to consistent data, therefore, and also admitted that many evolutionary relationships among vertebrates have been intractable.  But the statement that “The results extend our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization” was all the news media needed to promote Darwin.  Live Science trumpeted, “Gunk in T. Rex Fossil Confirms Dino-Bird Lineage.”  Ditto for Science Daily.  For a contrasting view, see what David Tyler wrote on Access Research Network.

1.  Organ, Schweitzer, Zheng, Fremark, Cantley and Asara, “Molecular Phylogenetics of Mastodon and Tyrannosaurus rex,” Science, 25 April 2008: Vol. 320. no. 5875, p. 499, DOI: 10.1126/science.1154284.

We read the fine print, not the bold headlines.  If you don’t mind a wading expedition through muddy jargon, you will no doubt notice how much fudging and guesswork goes into these kinds of analyses:

Bayesian, likelihood, parsimony, and distance methods were used to generate evolutionary trees.  In the Bayesian analysis, the posterior distribution of trees reconstructed all extant groups in generally agreed-upon relationships (the posterior probability of clades ranged from 0.80 to 1.00), with the exception of green anole (A. carolinensis), which is inferred here to lie at the base of amniotes instead of grouping as the sister taxon to alligator and birds (archosaurs) (Fig. 1).  LC/MS/MS from tryptic digests produces fragmentary protein sequence data; however, we found unequivocal support (posterior probability of 1.00) uniting mastodon with elephant as members of Elephantinae, which together group with tenrec (E. telfairi) as members of the mammalian group Afrotheria.  Maximum likelihood produces the same groupings, although with less support (approximate likelihood ratio test; aLRT = 0.855 for Elephantinae and 0.872 for Afrotheria).  Maximum parsimony analysis also groups mastodon, elephant, and tenrec together (fig. S1, B to D).  For the T. rex sample, we used five peptide sequences from collagen {alpha}1(I) and one from collagen {alpha}2(I) for a total of 89 amino acids (Fig. 1).  The T. rex clusters within the Archosauria (posterior probability of 0.92), more closely related to birds (chicken and ostrich, 0.9) than alligator, although a lack of informative sites in the ostrich and T. rex leaves Dinosauria unresolved.  The likelihood tree is identical to the Bayesian tree, except for higher support at these locations in the tree (aLRT = 0.969 for Archosauria and 0.907 for Dinosauria).  Branch lengths (expected rates of change per site) indicate a relatively stable and uniform rate of evolution, lacking evidence for a deviation from a molecular clock.  Maximum parsimony analysis also groups the T. rex with the chicken and ostrich, although bootstrap support is low (fig. S1, B to D).  Neighbor joining groups the T. rex with the birds, but miscalculates the branching order and misplaces alligator, mastodon, and several extant organisms (fig. S1, B to D).

If a group of scientists sets out to find Darwin in the trees, with funding from the NIH, NSF and two private foundations, is it any wonder they find him?  Doubtless the funding might dry up if they came back saying, “Sorry, all we found was intelligent design.”  It may be worthwhile to recall that phylogenetic algorithms are subject to many problems.  Bayesian analysis, for instance, is a garbage-in, garbage-out method that is not without serious epistemological issues (02/05/2004 bullet 4, 10/01/2005).  Using D for Darwin and G for Garbage, we propose three new acronyms in addition to the famous GIGO (garbage in, garbage out):

  • DIDO: Evolutionary reasoning, from assumption to conclusion.
  • GIDO: The belief that Darwin’s mind arose from chaos.
  • DIGO: How creationists view evolutionary inference.
    It is clear that the team gravitated to the methods that supported their preconceived notions about evolutionary ancestry.  Even the three most concordant results, however, left important relationships unresolved, and placed dinosaurs closer to chickens than to other reptiles (alligators, anole lizards, and perhaps other dinosaurs).  How well does that “confirm” evolution?  Readers may wish to review earlier entries about problems with tree-building algorithms (03/19/2007, 11/26/2002, 06/13/2003, 11/14/2005, 01/26/2008, and 07/25/2002).
        Aside from the fact that even strict creationists would expect to find many similarities in proteins used for similar functions, this paper strained at the gnat of similarity between 89 amino acids in one protein, using it to make sweeping generalizations about evolution, while swallowing the camel of the problem of soft tissue preservation.  When a person tries to hide a camel by swallowing it, however, it is hard for alert bystanders not to notice.
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Categories: Dinosaurs, Fossils, Mammals

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