Why the religious will never admit you won the argument (and why they don't care)

[SteveII]

For those that want to know more about this subject, they should read about it from a scientist and not the interpretation of a non-scientist (me). 

Antonis Rokas , Sean B Carroll
http://journals.plos.org/plosbiology/art...io.0040352

I don't see any support in this document for the claims made by SteveII. THe document seems (to my untrained eye) to raise some questions on the details of the TOL and the ability of certain kinds of statistical analysis to resolve clear lineages / branches. This may turn out to be an issue with the datasets, or the limitations of the statistical analysis itself. That the TOL can't be resolved into a perfect tree (rather, some areas are more cloudy) doesn't have to be a problem or a 'gap' in the theory itself. It certainly doesn't provide anything that contradicts the theory of evolution. I don't think anyone ever claimed to have completed the TOL - in fact Dawkins says this won't happen for another 10 years.

If the analysis had shown that the TOL simply didn't exist, and that there were just distinct species with no apparent lineage or organised relationships, then the analysis would have suddenly become a subject of huge interest and would have been pulled apart by scientists eager to verify (or reject) the findings.

I didn't read it quite the same as you. They quoted Dawkins at the beginning to point out the current viewpoint and then ended the intro with:

Here we discuss how and why certain critical parts of the TOL may be difficult to resolve, regardless of the quantity of conventional data available. We do not mean this essay to be a comprehensive review of molecular systematics. Rather, we have focused on the emerging evidence from genome-scale studies on several branches of the TOL that sharply contrasts with viewpoints—such as that in the opening quotation—which imply that the assembly of all branches of the TOL will simply be a matter of data collection. We view this difficulty in obtaining full resolution of particular clades—when given substantial data—as both biologically informative and a pressing methodological challenge. The recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics. [emphasis added]

And then they ended with:

The identification of clades is of fundamental importance to molecular systematics [63]. It is perhaps for this reason that over the years, systematists have emphasized reconstructing the topology of trees, while placing much less emphasis on the temporal information conveyed by unresolved stems. Currently, phylogenetic bushes are considered experimental failures. But that is seeing the glass as half empty. A bush in which series of cladogenetic events lie crammed and unresolved within a small section of a larger tree does harbour historical information [33,56]. Although it may be heresy to say so, it could be argued that knowing that strikingly different groups form a clade and that the time spans between the branching of these groups must have been very short, makes the knowledge of the branching order among groups potentially a secondary concern.