March 30, 2004 | David F. Coppedge

Whoops; Coelacanth Not in the Family Tree

Sorry; they looked like they were evolving.  The ungainly coelacanth, long thought extinct but then discovered alive and well in the Indian Ocean in the 1920s, had bony fins that evolutionists presumed were forerunners of limbs.  Now, a report in PNAS1 says lungfish instead were the distant ancestors of us and our fellow land vertebrates.  The authors, Brinkmann et al., considered their work a valiant attempt to solve a big problem:

The colonization of land by tetrapod ancestors is one of the major questions in the evolution of vertebrates.  Despite intense molecular phylogenetic research on this problem during the last 15 years, there is, until now , no statistically supported answer to the question of whether coelacanths or lungfish are the closest living relatives of tetrapods.

They compared the DNA of two genes in three lungfish groups and with coelacanth, and despite some puzzling results, tipped the ancestry score to the lungfish based on “high bootstrap values, Bayesian posterior probabilities, and likelihood ratio tests.”

1Brinkmann et al., “Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0400609101, Published online before print March 22, 2004.

OK, so they get their publication in one journal before someone shoots it down somewhere else.  You can pick the genes that give you the results you want, if you massage them thoroughly with heavy doses of imagination while under the influence of Darwin whiskey.
    What a crazy way to do science.  Now anybody with a PhD and a knowledge of fancy jargon and mathematical hand-waving tricks can build a fictional account of the unobservable past that can never be proven.  As long as it might be true (provided we can massage away the protruding bones) it’s good enough to be published.  Should this be called science, which most people assume has something to do with discovering truth?  Look at this example of what these authors do in their paper when one of their methods doesn’t produce the desired result.  The details don’t matter, the medium is the massage:

The ML-based [Maximum-Likelihood] method (QP) shows generally high support values for all inferred branches, with three exceptions: (i) the nodes supporting the monophyly of lungfishes, (ii) the node supporting the sistergroup relationship of tetrapods and lungfishes, and (iii) the node supporting the monophyly of the Sarcopterygii (44%).  Part of the problem can be explained by the surprising result that TREE-PUZZLE supports an obviously artificial monophyletic group of Neoceratodus and the coelacanth with the highest value of 48% in this region of the tree.  It is known that the TREE-PUZZLE program is rather sensitive to pronounced differences in evolutionary rates because of the quartet approach.  The African and the South American lungfishes evolve quite fast , and the Australian lungfish and the coelacanth sequences evolve comparatively slower.  This constellation of pronounced differences in evolutionary rates may lead to an artificial grouping of sequences with similar evolutionary speed (usually the slowly evolving ones).  Often a more basal position of the fast evolving lineages due to long branch attraction effects will result, because these faster sequences are “pulled” toward the faster evolving sequences at the root, i.e., outgroup of the tree.  This explains why the highest support of QP among basal Sarcopterygii (48%) seems to favor a clearly incorrect grouping of Neoceratodus and the coelacanth, again supporting the notion that QP might not be the most appropriate method for this phylogenetic problem.

So we’ll just explain away the data that don’t fit our preconceived “notions” and adjust the imaginary parameters (evolution rates) till we get a semblance of congruence.  Tweak, tweak, tweak.  The rest of the article uses copious wiggle words – might, probably, possibly, support, etc.  Molecular phylogeny is just a game Darwin Party members like to play, because it has no possibility of a winner (see 07/25/2002 headline).
    For more on the winless game of guessing tetrapod evolution, see 07/30/2002, 12/03/2003 and 08/09/2003 headlines.

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