Allright, forget the fossils

Here is one way of looking at the Theory of Evolution.You can arrange organisms by their morphology, so that they form a tree.You can arrange organisms by their ancestry, so that they form a tree.You can arrange organisms by their genetics (DNA), so that they form a tree.ToE says that these are all the same tree.The primary evidence for ToE is in genetics and reproductive biology, which demonstrates the processes by virtue of which these are the same tree.Secondary evidence is in the form of using ToE to make predictions, and checking whether those predictions are confirmed. The basic idea behind predictions is simple. Given any one of morphology, ancestry, genetics you can locate the organism in the tree. Then, from the location in the tree you can predict the other two (of morphology, ancestry, genetics).The best secondary evidence comes from field biology - examining species found in nature, where morphology and genetics can be checked, and ancestry can be partially checked.Here is how fossils fit in. They provide partial information on morphology. Dating of the fossil gives partial information on ancestry. With these two you can find an approximate location in the evolutionary tree. That allows the estimation of other information about the organism that was fossilized. It is mainly an exercise in the tentative reconstruction of natural history. It is indirectly supportive of ToE in that the method works.

In many cases it cannot be determined. But it surely can be in the lab or in laboratory like conditions (plant and animal breeding for example).

I was trying to describe ToE in terms of data analysis.Science idealizes. We say that the temperature is a real number. But when I read a thermometer I only get a range of possible values, due to the presence of measurement error. If we take statistical thermodynamics seriously, then there is no exact real number for a temperature, at best there is a probability distribution. Still, the idealization works well and is simple to apply.In the same way, the idea of a tree of organisms is an idealized picture. The data is usually blurry, giving an approximate location in the tree. We typically collapse a whole species into a blurry spot in the tree.But the idealized picture still explains how the prediction works. The consequence of blurriness is that if the data is blurry, then the predictions are blurry. This is the crux of the creationist-evolutionist debate.The tree we can build from "who gave birth to who" is a local tree. Based on reproductive biology, we can see that every organism fits into such a small local tree.Side note (for the lurkers): I should clarify that "tree" is being used here in the mathematical sense (from graph theory), not the thing growing in your back yard.What reproductive biology cannot tell us, is whether there is one huge tree containing all organisms, or there are multiple disconnected trees. ToE claims a single tree, and creationists claim multiple small trees. That's their argument of "micro-evolution but not macro-evolution".If there are multiple disconnected small trees, then prediction should work as I described it within any of those small trees. But there is no obvious reason to expect prediction to work across trees. That prediction works quite well overall, is therefore strong evidence for a single large tree.

There are different statements of the theory, and they might not all agree on this.As far as how the theory is used, it doesn't much matter whether it is one tree or few trees (say a tree per phylum). I agree with you that the evidence favors one tree.

When there is an apparent disagreement over classification between the genetic and morphological data, would not this be for two very close location which most creationists would agree are in the same tree?