"ToE" claims that the organisms we see today are the result of natural selection operating on changes over time on populations that all arose from one individual. The argument over ToE is over one tree versus unknown number of trees. Evolution is not denied by creationists who realize some form of super evolution had to occur with the ark pairs to give us the diversity of organisms we see today. In order for ToE to be correct there needs to be ONE tree because the genetic evidence for it is the same genetic mechanisms throughout all life-forms (minus the pesky virii :-)). This seems to be the case. However I'd also like to point out that in many areas of biology (this includes academia), the emphasis has shifted so much to genetics that there are very few morphologists anymore. After all, who wants to be an old museum specimen (I'm very proud of my morphologist self thank you :-D) when you can be the superman molecular biologist? As a result, especially with the impressionable youngsters, the benefits of genetics are always told and many of the pitfalls are left out. For example, which tree do we trust when the genetics give one that differs from the morphological one? Why would we trust a specific tree? For those who don't think this occurs a great source is:
Losos, J.B., T.R. Jackman, A. Larson, K. de Queiroz, and L. Rodriguez-Schettino. 1998. Contingency and determinism in replicated adaptive radiations of island lizards. Science 279:2115-2118.
Other problems are which sequence is truly representative? How does this sequence change over Earth History and is it reliable in all organisms. What about selfish genes and gene hopping? What degree of convergence occurs in genes? Where is embryology in all this?
The trees we get using ToE are all based on the assumption that there is one tree. Trees are not evidence in any form but are the completed proposal of history. In the literature the tree (route evolution took) is argued, not whether or not using one tree is justified. They work because so many of the methods assume that like organisms are related to one another (both morphologically and genetically) If both sides say that the common genetic mechanisms exist because of either common descent or common designer, how can you really predict anything differently in this realm? This is by the way, without the aid of fossils and radiometric dating as given below. This is also done without taking behavior and ecology into consideration..
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