There are even some ideas of how this may have happened. In Debating Design, Bruce Weber and David Depew point out that lightsensitive enzyme systems can be found in bacteria, and these systems are probably very ancient. The bacteria don't use them for vision, but as part of their metabolic (energy-gaining) processes. Proteins in the human lens are very similar to metabolic enzymes found in the liver. So the proteins that make the eye did not start out as components of a system whose purpose was vision. They arose elsewhere and had quite different `functions'. Their form and function were then selectively modified when their rudimentary light-sensing powers turned out to offer an evolutionary advantage.
Although we now know quite a lot about the genetics of the human eye, no biologist claims to know exactly how it evolved. The fossil record is poor, and humanoid eyes don't fossilise (though trilobite eyes do). But biologists can offer simple reasons why and how the eye could have evolved, and these alone are sufficient to demolish claims that its evolution is impossible in principle because the eye's components are interdependent and removing any one of them causes the eye to malfunction. The eye did not evolve one component at a time. Its structure evolved in parallel. The instigators of more recent revivals of Paley's doctrine, albeit in less overtly theist tones, have taken on board the message of the eye as a specific case ... but its more generic aspects seem to have eluded them. Darwin's discussion of the eye, and the Nilsson-Pelger computer experiment, are not limited to eyes. Here is the deeper message. When confronted with a complex living `mechanism', do not assume that the only way it can evolve is component by component, piece by piece. When you see a watch, do not think of hooking up springs and adding cogwheels from some standard box of spare parts. Think more of a Salvador Dali `soft watch' that can flow and distort, deform, split apart, and rejoin. Think of a watch whose cogwheels can change shape, grow new teeth, and whose axles and supports evolve along with the cogs so that at every stage the whole thing fits together. Think of a watch that may have started out as a paper clip, and along the way became a pogo-stick. Think not of a watch that does and always did have a single purpose, which was to tell the time. Think of a watch that once held sheets of paper together and could also be straightened out to form a toothpick, and which later turned out to be great for bouncing, and started to be used for measuring time only when someone noticed that its rhythmic movements could chart the passing seconds.
Yes, proponents of intelligent design understand the eye ... but only as one example, not as the basis of a general principle. `Oh, yes, we know all about the eye,' they say (we paraphrase). `We're not going to ask what use half an eye is. That's simple-minded nonsense.' So instead, they ask what use half a bacterial flagellum is, and thereby repeat the identical error in a different context.
We owe this example to Michael Behe, a biochemist who was baffled by the complexity of bacterial flagella. These are the `tails' that bacteria use to move around, tiny `screws' like a ship's propeller, driven by a rotary molecular motor. Some forty proteins are involved in making such a motor, and if you miss any of them out, it won't work. In his 1996 Darwin's Black Box, Behe claimed that the only possible way to make a flagellum was to encode the whole structure, in advance, in bacterial DNA. This code could not have evolved from anything simpler, because the flagellum is `irreducibly complex'. An organ or biochemical system is said to be irreducibly complex if removing any of its parts causes it to fail. Behe deduced that no irreducibly complex system can evolve. The example of the bacterial flagellum quickly became a cornerstone of the intelligent design movement, and Behe's principle of irreducible complexity was promoted as an unavoidable barrier to the evolution of complex structures and functions.
There are several excellent books that debate intelligent design: we've mentioned two earlier in a footnote. It's fair to say that the antis are winning the debate hands down - even in books edited by the pros, such as Debating Design. Perhaps the biggest problem for the pros is that Behe's fundamental concept of `irreducible complexity' has fatal flaws. With his definition, the deduction that an irreducibly complex system cannot evolve is valid only if evolution always consists of adding new parts. If that were the case, then the logic is clear. Suppose we have an irreducibly complex system, and suppose that there is an evolutionary route leading to it. Focus on the final step, where the last part is added. Then whatever came before must have been a failure, so it couldn't have existed. This is absurd: end of story.
However, evolution need not merely add identifiable components, like a factory-worker assembling a machine. It can also remove them - like a builder using scaffolding and then taking it down once it's done its job. Or the entire structure can evolve in parallel. Either possibility allows an irreducibly complex system to evolve, because the next to last step no longer has to start from a system that lacks that final, vital piece. Instead, it can start from a system with an extra piece, and remove it. Or add two vital pieces simultaneously. Nothing in Behe's definition of irreducible complexity prohibits either of these.
Moreover, `fail' is a slippery concept: a watch that lacks hands is a failure at telling the time, but you can still use it to detonate a timebomb, or hang it on a string to make a plumb-line. Organs and biochemical systems often change their functions as they evolve, as we've just seen in the context of the eye. No satisfactory definition of `irreducible complexity' - one that really does constitute a barrier to evolution - has yet been suggested.
According to Kenneth Miller in Debating Design: `the great irony of the flagellum's increasing acceptance as an icon of the antievolutionist movement is the fact that research had demolished its status as an example of irreducible complexity almost at the very moment it was first proclaimed'. Removing parts from the flagellum do not cause it to `fail'. The base of the bacterial motor is remarkably similar to a system that bacteria use to attack other bacteria, the `type III secretory system'. So here we have the basis of an entirely sensible and plausible evolutionary route to the flagellum, in which protein components do get added on. When you remove them again, you don't get a working flagellum - but you do get a working secretory system. The bacterial method of propulsion may well have evolved from an attack mechanism.
To their credit, proponents of intelligent design are encouraging this kind of debate, but they have not yet conceded defeat, even though their entire programme rests on shaky foundations and is collapsing in ruins. Creationists, desperate to snatch at any straw of scientific respectability for their political programme to lever religion into the American state school system, [1] have not yet noticed that what they are currently taking as their scientific support is falling apart at the seams. The theory of intelligent design itself is not overtly theist - indeed its proponents try very hard not to draw religious conclusions. They want the scientific arguments to be considered as science. Of course that's not going to happen, because the theist implications are a little too obvious - even to atheists.
There are some things that evolution does not explain - which will gladden the heart of anyone who feels that, Darwin notwithstanding, there are some issues that science cannot address.