Phylogenetic analyses are inconsistent (Talk.Origins)
Modern versions of the phylogenetic "tree of life" are based on DNA and other molecular analyses. Inconsistent and bizarre results based on different molecular analyses "have now plunged molecular phylogeny into a crisis" (Wells 2000, 51).
- Wells, Jonathan, 2000. Icons of Evolution, Washington DC: Regnery Publishing Inc., pp. 49-54.
(Talk.Origins quotes in blue)
1. A few inconsistencies are to be expected, because biology is messy. Genes need not always evolve at the same rate in different lineages. Some molecules may converge as a result of selection or chance. Horizontal gene transfer occasionally occurs. Such exceptions will be rare, but there will be a few of them among the vast body of consistent results.
Nice theory, but Wells's entire point is that such cases are not rare but rather make up the general pattern of results.
Most inconsistencies can be resolved by basing an analysis on multiple genes.
Except for the fact that Wells offers several references showing that the larger the number of genes or molecules, the bigger the problem.
Other inconsistencies will occur as a result of methodological and interpretive mistakes. Phylogenetic analysis is a very complex subject; people who do not understand it well cannot be expected to get it right all the time. Publishing one's methods and results allows others to catch mistakes.
Wells clearly deals with this as well. It turns out that their frequency and statistics eliminate methodological and interpretive mistakes as a general explanation.
Creationists looking for inconsistencies can dishonestly pick out the few there are while disregarding the vast body of consistent results and the reasons for the inconsistencies.
While this is theoretically possible, Wells does not do this. Yes, he cites a few examples, but they are intended only as illustrations.
2. Some claimed inconsistencies are really consistent.
Wells's case rests on more than just a few examples, and those he used were just illustrations. Given the fact that theories tend to change from time to time, it is likely that some previous inconsistencies will become consistent.
Wells, for example, cited a study which "placed sea urchins among the chordates" (Wells 2000, 51), but sea urchins (and echinoderms in general) do group with chordates as a sister group.
Sea urchins may be grouped in a broader category with chordates, but they are still not chordates, though some genetic similarities suggest that they are. Talk Origins is grasping at straws here.
Wells (2000, 51) also cited another study that "put cows closer to whales than to horses," which is also entirely consistent with genetic, morphological, and fossil evidence.
Talk Origins gives absolutely no basis for cows being closer to whales than to horses. What evidence are they referring to?
The claim that morphological evidence puts a cow closer to a whale than a horse is absurd, to say the least. There are clearly far more morphological differences between a cow and a whale than a cow and a horse.