Behe on the flagellum, an irreducibly complex biological system that baffles scientists:
http://www.arn.org/docs/behe/mb_brresp.htm
What has biochemistry found that must be explained? Machines--literally, machines made of molecules. Let's look at just one example. The flagellum is an outboard motor that many bacteria use to swim. It consists of a rotary propeller, motor, and stationary framework. Yet this short description can't do justice to the machine's full complexity. Writing of the flagellum in Cell, Lucy Shapiro of Stanford University marvels, "To carry out the feat of coordinating the ordered expression of about 50 genes, delivering the protein products of these genes to the construction site, and moving the correct parts to the upper floors while adhering to the design specification with a high degree of accuracy, the cell requires impressive organizational skills." Without any one of a number of parts, the flagellum does not merely work less efficiently; it does not work at all. Like a mousetrap it is irreducibly complex and therefore cannot have arisen gradually.
The rotary nature of the flagellum has been recognized for about 25 years. During that time not a single paper has been published in the biochemical literature even attempting to show how such a machine might have developed by natural selection. Darwin's theory is completely barren when it comes to explaining the origin of the flagellum or any other complex biochemical system.
The sterility of Darwinism indicates that it is the wrong framework for understanding the basis of life. As I argue in my book, an alternative hypothesis is both natural and obvious: systems such as the flagellum were intentionally designed by an intelligent agent. Just as in the everyday world we immediately conclude design when we see a complex, interactive system such as a mousetrap, there is no reason to withhold the same conclusion from interactive molecular systems. This conclusion may have theological implications that make some people uncomfortable; nonetheless it is the job of science to follow the data wherever they lead, no matter how disturbing.