Many people think that science is done in a theological vacuum. However, it is not. Take for instance, a recent paper on the flagellum - Coordinating assembly of a macromolecular machine:
Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system. We only need to be reminded that evolution demands that changes occur on the existing structure — no starting from scratch. It is fair to say that we are at long last making a dent in our understanding of how this evolutionary process might have occurred for the reducibly complex bacterial flagellum and the beautiful result it has produced.
So, the reason we are not resorting to design is not because it doesn't evidence design, but rather because a designer would not have done it this way! That is a statement of both theology and engineering that the authors have no grounds to say.
Here's an article on the flagellum:
Is the flagellar motor unique?
Yes and no. As a device that powers flagellar rotation, yes. As a device composed of rings, rods, and external filaments, no. There is a homologous structure, called the needle structure, assembled by the same kind of transport apparatus, used by pathogenic species (such as Salmonella) to inject virulence factors into eukaryotic cells. Some argue that the flagellar rotary motor evolved from the needle structure, but it was probably the other way around,
since flagellated bacteria existed long before their eukaryotic targets. Perhaps they evolved from a common ancestor. What was the rotary motor doing before the helical propeller was invented, if indeed that was the order of events? Serving as a secretory apparatus that acquired the ability to spin? Packaging polynucleic acids into virus heads? Food for thought.
So now, not only is the flagellum IC, but even the supposed "precursor systems" don't make sense until long after the flagellum supposedly developed. What we are finding, over and over, is that there is no such thing as a simple life form. Therefore, we can conclude that those who view evolution as progressing from simple to complex are doing so because of theological commitments, not because of evidence. I have no problem with people engaging in science from theological commitments (it's actually impossible not to), I just wish they would admit it.