You have changed what you said. Your previous claim is that evolution is not an explanation for life’s diversity as it’s claims cannot be directly tested. Now you say that the claim of evolutionary transitions as a complete explanation of the diversity of life. Linguistically, it is subtle, but it makes all the difference. I don’t think evolutionary theory, nor any other theory for that matter, is a ‘complete’ explanation of anything. Nevertheless, I do think that the theory proposes hypothesis that are testable and the are indeed tested (which was my previous objection).
I never said it did.
Indeed, that’s convergent evolution. Or are you going to complain that no theory should allow of auxiliary hypotheses to explain exceptions that were not predicted by the primary hypothesis?
You have to careful with this. To name one example, sequences that experience more mutations than others, it is statistically likely that they become convergent more similar than other sequences each are otherwise more closely related to. This effect is known as ‘long branch attraction’ and it is well-known.
I have read about this. I am happy that ID-proponents are finally attempting to give a mechanism of design, rather proposing for some vague concept with no principles. While I don’t have the time to go over the full paper in dept, I will point out one major issue that sticks out to me. Here they propose that the designer are compelled by design constraint to reuse parts or modules, in order to solve similar functional problems, in such a manner that would produce a pattern, not just akin to a nested hierarchy, but actually produce pattern that fits much better as it also explains things that would otherwise be considered as homoplasy. Firstly, this appears to exclude an omnipotent designer, as this principle implies the designer is subject to constraints. Although that is just a side note. My main problem is that organisms don’t seem to reuse parts in the manner that is proposed. Not even regarding “instances of module reuse across taxonomic boundaries”, which they think is especially better explained by their design principle rather than common descent. Let’s look at one example they use in the paper, marine mammals. They all have fins that functions for swimming in water just like other aquatic vertebrates. The similarity in shape of all fins are clearly constrained by having to function as a hydrodynamic foil in water. However, they don’t appear to be “reused modules”, at least not in the sense that they propose. Instead, marine mammals have the same underlying bone structure as you and me; humerus, ulna, radius, (meta)carples, and digits. In some cases, such as manatees, they also have fingernails. They clearly appear to be “reused” or (more appropriately) modified from the limbs of terrestrial tetrapods, rather than from something that already served the same function. This is even more striking in the case of penguins (not mammals, but still). The underlying structure of their fins suggest a modification not just from tetrapod limbs but from bird wings specifically. Another thing to note are the absence of ‘reuse’ that one could expect otherwise. For example, why do none of the marine tetrapods have gills ‘reused’ from fish or from anything else that breathe oxygen from water in addition to breathing oxygen from air with lungs? Note, I did not say ‘why not gills instead of lungs’. I understand that lungs may have some benefits over gills, but they are not mutually exclusive. So, even such cases of homoplasy, they are still very consistent with the nested pattern of common descent, and not with the design principle to reuse modules that already fulfilled the same functions.
