“If a designing intelligence acted discretely in the history of life, the various subdisciplines of biology should show evidence of polyphyly.”
Again, Meyer shows a degree of knowledge about what the proposed intelligent designer would or would not do. Such knowledge is not accessible to or testable by the scientific community in general. In this case, Meyer suggests that the designing intelligence would have designed life on earth through several different originating species and not one common ancestral source, though it’s not clear why. Polyphyly could also conceivably be due to abiogenesis being more probable than we currently think, a possibility that cannot yet be ruled out.
It is interesting to speculate what would constitute evidence of polyphily. Would a major discontinuity in the fossil time sequence suffice? Or would it require finding life based on different amino acids than the 20 used in terrestrial life? Or life with a different chirality of biomolecules? Or life based on a different set of nucleotides than the 4 that comprise all known life that has been discovered so far? Meyer states “Since intelligent agents have the freedom to combine modular elements and subsystems in unique ways from a variety of information sources, we should expect phylogenetic analyses of diverse systems and molecules to generate some conflicting trees.” In other words, does he mean that if we cannot resolve conflicts in putting together a phylogenetic tree, we have evidence of polyphyly? It may be true that a polyphyletic system would have multiple discontinuities in its tree of life, but proving that conflicts are due to polyphyly wouldn’t be that simple.
In any case, it is noteworthy that not even a hint of polyphyly has been discovered so far. If polyphyly ever is proven, it would indeed be a major change in understanding of life on earth. It would not necessarily strengthen the case of ID since there is no necessary relationship between the two.