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Intelligent design scholar Michael Behe has argued that certain biological systems, such as bacterial flagella, blood clotting machinery, and the vertebrate immune system, are "irreducibly complex": they consist of multiple subsystems, the removal of any one of which would render the system nonfunctional. He argues that such systems must have been designed by an intelligent entity, because none of the components could have evolved in the absence of the others [Behe1996, pg. 39-139]. Behe offers a homey example to illustrate his concept of irreducible complexity: the mousetrap. He notes that a mousetrap consists of five individual parts: (a) platform, (b) spring, (c) hammer, (d) hold-down bar, and (e) catch. If any of these parts is removed, the mousetrap cannot function to catch mice. Thus it must have been designed by an intelligent entity, because none of the four parts could "evolve" in the absence of the others.
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].
With regards to Behe's example of the bacterial flagella, researchers recently found that its DNA sequence is almost identical to that of a "needle" that certain bacteria use to insert toxins [Jones2008; Miller2004]. Kenneth Miller has shown in addition that several components of the flagellum have other selectable functions [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].
A premier example frequently mentioned by both creationist and intelligent design writers is the human eye. These writers insist that a high-resolution light gathering system, such as retina, would be useless without a lens, and vice versa. Yet even Charles Darwin proposed a multi-step scenario of how eyes might have developed, beginning with a photosensitive cell, progressing to an optic nerve surrounding pigment cells, and finally concluding with muscles that could contract around the lens. What's more, within the animal kingdom one find can a wide range of eye designs, including numerous instances that are significantly better than human eyes. Octopuses and other mollusks, for example, have optic nerves that emerge from the back of the retina, thus avoiding the blind spot that afflicts human vision. Similarly, hawks have a visual acuity rating of 20/5, significantly better than the 20/20 vision of humans. Owl eyes are 50 to 100 times more sensitive to light at nighttime than are humans [Isaak2007, pg. 65, 94-95].
In a similar way, scientists have found that most of the proteins involved in the blood clotting system are genetically similar and most likely are the result of gene duplication [Fairbanks, 2007, pg. 150-156]. With regards to the Behe's claim that the vertebrate immune system is irreducibly complex, journalist Lauri Lebo's account of the proceedings in the 2005 trial on intelligent design in Dover, Pennsylvania provides an amusing illustration of the difficulties involved [Lebo2008, pg. 153-154]:
... 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].