“If the flagellar motor was intelligently designed and the type-3 secretory system devolved from it, the genes that code for the bacterial flagellar motor should be older than those that code for the proteins in the T3SS, and not the reverse. Alternatively, if the T3SS and the flagellar motor arose by design independently, T3SS should have unique (nonhomologous) genes that are not present in the genome for the flagellar motor.”
The debate on the irreducible complexity of the flagellar motor has gone on for many years. This is one more episode in that seemingly endless discussion, and does not need extensive discussion here. The bright spot in the discussion is that it is stimulating more research to focus on paths in which the motor may have developed. Until the specific steps in the development of the motor are discovered, any prediction of what could or couldn’t have taken place is rather speculative. It is extremely difficult to show evidence that something could not have evolved. We do not know enough about all possible paths of evolution. Biologists now understand that biomolecules do not need to evolve incrementally, one nucleotide at a time. Rather, they may more often be formed from modifications of larger segments such as an entire exon at a time.
It is also extremely difficult to determine how a biomolecule did evolve since there is no detailed fossil record of biomolecules that existed in the past and the genetic evidence is necessarily indirect, if it is available at all. The value in the discussion lies in our discovery of possible evolutionary paths that we did not previously understand. This prediction won’t settle the matter whatever the results may be.