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On the general subject of accuracy in molecular phylogenies see Theobald 2002b and for recent work on phyla evolution and metazoan molecular phylogenies, which are quite certainly not in crisis, see recent articles in places "The affinities of all the beings of the same class have sometimes been represented by a great tree. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications." (Darwin, , Wells has a ball with recent scientific debates over whether or not lateral gene transfer mixed up ancient genomes so much that deepest branches of the tree are mixed up.
Basically, some scientists have proposed that the idea of a single "last common ancestor" should be replaced with the idea of a "last common gene pool" that the extant three domains of of life -- eukaryotes, archaea and eubacteria, in one classification scheme -- gradually emerged from.
The original Miller-Urey experiment, despite its limitations, is also repeatedly cited in modern scientific literature as a landmark experiment.
Amundson (2001) critiques the circularity charge well: This criticism relies on a faulty view of what scientific definition amounts to.
A scientific definition is not a semantic stipulation that creates an analytically true statement (i.e.
cone snail venoms are a fantastic example of rapid sequence divergence under selective pressure; see Espiritu et al., 2001).
And if these changes occur often enough then getting accurate clock dates, particularly for distant events, will be very hard.
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Lankester and Mayr consider ancestry to explain patterns of homology, and stress that fact by making it the definition.