First, it is correct that in very rare circumstances a mutation may be adaptive rather than harmful or neutral. This does not mean that it is information-creating. For example, a bacterium may become resistant to a toxin because a mutation knocks out its ability to metabolize the specific chemical. Similarly, a random change in my word processor program might on rare occasions improve its performance if it disables some part of the program which is causing trouble. Or you may actually “fix” a stuttering radio by hitting it, thus clearing some short circuit. This is no way to build a television set or write advanced software. In any case, creative evolution would require massive and continuing information creating, something far beyond even the most optimistic reading of the evidence.
Second, your argument about what biologists call “homology” mixes two distinct questions: 1) “What is the pattern of nature?”; and 2) “What is the cause of that pattern?” It is true that nature has a pattern of groups within groups, so that mammals are distinct from birds, vertebrates from invertebrates, and eukaryote cells (with nucleus) from simpler prokaryote cells. The whole subjection of classification is intensely controversial, but for simplification we may assume that the established groups are real and defined by common characteristics (homologies).
Very well; now what is the cause of this pattern? Similar patterns appear in systems that are designed by engineers. In fact, a zoologist named Tim M. Berra wrote a book citing the Corvette automobile as an example of descent with modification, since the various models of Corvettes are variations on a common basic plan. But of course this pattern results from engineering practice, and it is normal for intelligent designers (composers of music, for example) to employ variation on a common basic design. I call that confusion between design and natural descent “Berra’s Blunder,” and variations on it are pervasive in the Darwinian literature. One of them is your plagiarism example. What the instructor actually concludes is that the similarities are not the product of chance or natural law, but of a deliberate design to cheat.
When I wrote about this subject in Chapter 5 of Darwin on Trial, I said that common descent seemed a reasonable hypothesis in Darwin’s time to explain the pattern of nature. The problem is that, under the influence of materialist and positivist philosophy, the hypothesis quickly hardened into a dogma, so that it became the only conceivable cause of the pattern. Since then it has been common to cite the pattern as proof of the cause, just as you do.
If we treat common ancestral descent as a true hypothesis, and test it objectively against the evidence, it runs into problem after problem. Darwinists still cite embryology as confirmation, for example, but putative homologies do not necessarily stem from common embryonic pathways or common genes. The fossils don’t confirm the hypothesis either, when the fossil evidence is taken as a whole and the testing is done without Darwinian prejudice. The Darwinian practice is to search the fossil record selectively for any example that can be interpreted as a possible cousin to a hypothetical ancestor. Almost all the claimed examples come from vertebrate animals, where the fossil record is most sparse and imagination therefore has the most leeway. Test the hypothesis against a more complete fossil record, as with marine invertebrates, and you find variation within groups but no examples of continuous evolutionary change from one major group to another. When I debated the marine invertebrate specialist Niles Eldredge, he chose to illustrate creative macroevolution with hominid (ape-man) examples. If you have read his books, you will know why.
Finally, I note the accusatory tone of your messages. As a law professor I view this sort of thing professionally, and don’t take it personally. But I wonder if you are aware how unprofessional–and especially, unscientific–it looks to people who are inclined to doubt your theory. Scientists like to tell us they test everything, are continually looking for new evidence or new ways of thinking to upset established doctrine, and so on. No doubt this is true for many subjects, but on this topic any skepticism seems to be considered a sign of dishonesty or insanity. I’m told by witnesses that the science educators at the Kansas hearings made very liberal use of sarcasm and ridicule, and I honor the Kansas board members for standing up to the intimidation. I’d like to turn the debate from a culture war into a legitimate intellectual controversy, which would be exciting and informative for students, but I don’t see how that can be done until the academic establishment learns to treat the growing public skepticism with a measure of respect.