July 26, 2008 | David F. Coppedge

Dinosaurs Placed in Big Tree

Dinosaurs didn’t take advantage of the big rise in diversity at the end of the Cretaceous, say British researchers.  Their big “supertree” of dinosaur evolution shows that the dinosaurs were just evolving at a regular speed while flowering plants, social insects, birds and mammals were evolving like crazy.
    Science Daily and New Scientist were among popular media reports that printed the supertree diagram and stated the claim without question.  An examination of the original paper,1 however, shows something interesting:

In order to obtain a well-resolved tree, we undertook some post hoc taxon pruning where poorly constrained species, producing unacceptably high numbers (more than 5000) of equally probable supertrees, were removed.  Choosing a tree for diversity analyses was based on overall supertree support.

In fact, numerous subjective decisions were made to come up with the supertree.  The authors had to decide which fossils qualified as distinct species, for instance.  They also ran various tree-building software programs and had to decide threshold values for agreement: e.g., “To enforce MIX to run a compatibility analysis, the threshold parsimony option was set to 2.  One hundred heuristic searches were performed, and characters were weighted (as described above) using a specifically generated weight file.”  Subsequent paragraphs show even more subjectivity.  Here is one selection from the “Materials and Methods” section, to give a taste of the tweaking behind the result.  Some definitions of terms were added in brackets.

Phylogenetic shifts in diversification were detected using SYMMETREE v.  1.0 (Chan & Moore 2005).  Analyses of tree shape are biased when a group is paraphyletic [composed of some but not all members descending from a common ancestor], as a particularly speciose clade (in this case, birds) is represented by a single terminal (Archaeopteryx).  A modification was thus required in order to account for the absence of birds.  Although it was not feasible in the present contribution to include all birds, a hand-drawn phylogeny of the better-known Mesozoic taxa (72 species in total) was inserted at the node subtending Archaeopteryx +Jinfengopteryx, effectively making the tree a Mesozoic time slice.  (This placement of Jinfengopteryx is based on the original description (Ji et al.  2005), but more recent analyses, e.g. Turner et al. (2007), have placed it within Troodontidae.)  Polytomies [divisions into three or more parts] were treated as soft, with the size-sensitive ERM [equal-rates Markov] algorithm set to perform 10000 random resolutions per individual node and 1000000 random resolutions for the entire tree.  Internal branches within the phylogeny on which diversification shifts are inferred to have occurred were identified using the Delta-2 shift statistic.  This process was repeated for time slices of the whole tree as described in Ruta et al. (2007) to avoid violating the ERM model.

The tree was also fitted to the geological time scale, which assumes the very evolutionary story that the researchers were trying to discern.  Then, they added missing data (a kind of oxymoron), or “ghost ranges,” to get a smoother result:

Ghost ranges, minimal basal stratigraphic range extensions implied by the geometry of the phylogenetic tree, indicate missing fossil data, and allow us to correct diversity profiles for the group through the Mesozoic and to compare diversification rates, the proportional change in observed species richness as a function of time, at different points (figure 2b, solid line): note how the addition of ghost ranges smoothes the curve.  In particular, peaks in observed diversification rate in the Norian and Campanian-Maastrichtian (bins 3 and 12) are greatly reduced when ghost ranges are introduced.  This is a minimal correction that does not take account of unknown taxon ranges before the first appearance of the older of a pair of sister groups.  In addition, this correction does not address possible upward range extensions.  However, peaks in the earliest, Middle and Late Jurassic are still observed after introduction of ghost ranges (figure 2b, dashed line).

Did anyone ask whether selective judgments in software settings and subjective decisions about which species to include and exclude would generate reliable inferences about an unobservable past assumed to be over 100 million years ago?  Could this kind of tweaking be guaranteed, instead, to reproduce the authors’ own biases?
    The authors did try to correct for some known biases, such as sampling error.  They also discussed uncertainties that are hotly debated among evolutionists, such as whether diversification typically occurs early in a radiation or not.  “The fossil record of continental vertebrates is clearly patchy, with large temporal gaps between sampling horizons.  The seriousness of sampling bias is debated,” they also granted.  Even so, they had to admit, “It follows that the fluctuations in diversification rate may not necessarily reflect evolutionary signal, and these must be tested rigorously.
    When all was said and done, after repeated rounds of tuning the knobs, the signal that dinosaurs did not take part in the alleged “Cretaceous Terrestrial Revolution” was weak.  The popular science articles, though, reported it as a discovery of science.


1.  Lloyd, Davis, Pisani et al, “Dinosaurs and the Cretaceous Terrestrial Revolution,” Royal Society Proceedings B, 0962-8452 (Paper) 1471-2954 (Online), DOI: 10.1098/rspb.2008.0715.

You have just watched professional divination in action.  What these scientists did has no more relation to the true history of the world than the tea leaves in a fortune-teller’s bowl reveal about the origin of tea plants.  This is pure hocus, foisted on a gullible public under the guise of science (i.e., knowledge).  We provided detailed quotes from the paper to reveal how the trickery is done.  You don’t have to understand the jargon.  Just look at how subjective it is.  Why do the popular media publish the bottom-line claims of these wizards as if knowledge has just been gleaned from the world?  This is nothing but Darwinist imagination masquerading as scientific research.
    Notice how the project was saturated with evolutionary religion from start to finish.  The fossils (admittedly scanty) were first placed into the millions-of-years evolutionary story.  This step has already been falsified by the discovery of soft tissue in dinosaur bone, bringing the millions-of-years assumption crashing down (see 04/26/2008).  Unabashed by that inconvenient fact, the authors continued their vision quest by borrowing other published evolutionary-diviner chants and spells.  It’s only polite, after all, to reference one’s sources.  Then they used Darwin-divination software.  They selected only the tea leaves and lighting guaranteed to support their story.  They published their resultant horoscope in a Darwin-divination journal, then handed it to the Darwin-inebriated press to herald to the unwashed masses.  A colorful image of the Magic Supertree Diagram was displayed to lend an air of mystical authority to the announcement.
    All these shenanigans are designed to create a sense of numinous awe in the public consciousness.  Readers are supposed to bow down and confess that the diviners possess The Wisdom of The World, and that they are to be heeded instead of those wicked, nasty, evil, insane Creationists who proclaim a different message: that the complex bodies of birds, mammals, dinosaurs and insects reveal design, not chance, and that mythical “Cretaceous Terrestrial Revolutions” are incapable of forcing undirected matter to invent complex organs and functions.
    Get wise to the tricks of the wizards.  This is not science.  It’s not even magic.  It’s deception.  The deceivers who believe their own lies are the most to be distrusted.

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Categories: Dinosaurs

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