|Barred spiral galaxy NGC1672 [Courtesy NASA]|
Scientists counter that systems labeled as "irreducibly complex" by Behe can arise by natural evolution -- individual parts may arise separately, each useful in different context, and then later be combined into a larger system. As for Behe's mousetrap example, biologist Kenneth Miller observes that the various parts or subsets of parts of a mousetrap could function quite well in a different context: a tie clip (Miller often wears one), a key ring, a clipboard holder, a paper weight, and a nutcracker, among other things [Miller2003].
Proteins that make up the flagellum itself are closely related to a variety of cell surface proteins, including the pilins found in a variety of bacteria. A portion of the flagellum functions as an ion channel, and ion channels are found in all bacterial cell membranes. Part of the flagellar base is functional in protein secretion, and once again, all bacteria possess membrane-bound protein secretory systems. Finally, the heart of the flagellum is an ion-driven rotary motor, a remarkable piece of protein machinery that converts ion movement into rotary movement that males flagellar movement possible. Surely this part of the flagellum must be unique? Not at all. All bacteria possess a membrane protein complex known as the ATP synthase which uses ion movements to produce ATP. How does the synthase work? It uses the energy of ion movements to produce rotary motion. In short, at least four key elements of the eubacterial flagellum have other selectable functions in the cell that are unrelated to motility.
A similar assessment of the bacterial flagellum example is given by biologists Mark Pallen and Nicholas Matzke [Pallen2006]:
Three modular molecular devices are at the heart of the bacterial flagellum: the rotorstator that powers flagellar rotation, the chemotaxis apparatus that mediates changes in the direction of motion and the T3SS that mediates export of the axial components of the flagellum. In each module, the apparatus is fashioned from recycled parts that occur elsewhere in nature.
One plausible scenario for the evolution of the flagellum, several steps of which have been worked out in some detail, is presented in Mark Issak's book [Isaak2007, pg. 61-62].
... Rothschild [the prosecuting attorney] challenged Behe's dismissal that the "scientific literature has no answers to the question of the origin of the immune system."
"I see no Darwinian explanation for such things," Behe said, arguing that the immune system must therefore be irreducibly complex.
Rothschild trudged to the witness stand, plopping down a number of peer-reviewed articles and stacks of thick books on the subject of the evolution of the immune system. As he approached, Rothschild couldn't help but sneak a brief peek at the reporters in the jury box.
After stepping back, Rotschild asked, "Now, these articles rebut your assertion that scientific literature has no answers on the origin of the vertebrate immune system?"
"No, they certainly do not," Behe said. "My answer, or my argument, is that the literature has no detailed rigorous explanations for how complex biochemical systems could arise by a random mutation and natural section, and these articles do not address that."
"So these are not good enough?" Rothschild asked.
So Rothschild tried again. And again. He continued piling material onto the stand until the pile dwarfed the professor. By the time he was done, Rothschild had stacked up ten textbooks such as Origin and Evolution of the Vertebrate Immune System and fifty-eight articles from prestigious journals like Science, Nature, and Molecular Cell, all of them detailing research on the evolution of the immune system. Rothschild stared at Behe over the material. "Is it your position today that these articles aren't good enough?" he asked.
Attorneys would later refer to it as the Miracle on 34th Street moment.
Facts such as this ultimately convinced Judge John E. Jones, who presided over the Dover trial, to write in his decision, "We therefore find that Professor Behe's claim for irreducible complexity has been refuted in peer-reviewed research papers and has been rejected by the scientific community at large." [Jones2005, pg. 78-79].