We have a nested hierarchy that is best explained by common descent in the various kingdoms. We have the relationship between the various kingdoms that includes common coding for DNA to Protein, which could be a different coding. We have the establishment of speciation by such evidences as shared retroviral inserts and vestiges as well as the nested hierarchy. The denial of common descent across all kingdoms of life is normally done by people who completely deny those pieces of evidence as well, so their denial is not reasonable to weigh as being something to consider. So the common descent of all life is quite probable, probable enough to place it in the catagory of being the logical conclusion. The only other reasonable conclusion would be life started some small number of times other than one and evolved to what we see today . . . and that seems unlikely due to the common DNA coding, as I said above.
While that certainly is an argument it is not a LOGICAL one. It's far more of an EMPIRICAL argument based on some kind of abductive reasoning. Abductive reasoning, as you know, is a form of reasoning in which the truth of all of the inputs does not guarantee the conclusion. If, for example, you were a spirit that went around the Earth looking at rocks, minerals, dirt, water, etc., and suddenly happened upon a living creature you might feel that this is an unusual thing that requires some sort of an explanation.
Therefore, for your abductive reasoning to work, you need to establish not only that a nested hierarchy exists, but also that this is strange and thus in need of an explanation, and then indicate that common descent is the best explanation. Since other nested hierarchies exist (such as the military) that are not the result of common descent, or even the result of careful planning, I tend to disagree that nested hierarchies need explanation.
Second, you referred to speciation. Yet I wonder whether the exact definition of species is known, testable, and universally agreed upon. A simple definition of species (a group of creatures that can freely interbreed) immediately runs into a number of logical and practical problems. Many groups of animals that are nominally considered different species routinely interbreed (hybridization). In some cases the offspring are sterile, whereas in others they are not. The species definition also seems to exclude bacteria, as they don't interbreed among one another. Additionally there is the practical problem of looking at a Neanderthal fossil and that of a newly discovered fossil that may or may not be a Neanderthal. How can you determine whether the creatures were able to interbreed? Finally some species contain members that cannot interbreed (chihuahuas and St. Bernards) yet are classified as the same species.
Therefore, I generally reject the idea that speciation refers to any objectively knowable division and denied that supposed "speciation" events have any relevance.
