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.
[1] ' They themselves refer to this programme as the 'wedge strategy'. It is perfectly possible to agree with Darwin and his successors that the Earth is 4.5 billion years old, and that life has evolved, by purely physical and chemical processes, from inorganic beginnings - yet still find a place for a deity. Yes, in a rich and complex universe, all these things can happen without divine intervention. But ... how did that rich and complex universe come into being?
Here, today's cosmology offers descriptions of how (Big Bang, various recent alternatives) and when (about 13 billion years ago), but not why. String theory, a recent innovation at the frontiers of physics, makes an interesting attempt at `why?' However, it leaves an even bigger `why?' unanswered: why string theory? Science develops the consequences of physical rules (`laws'), but it doesn't explain why those rules apply, or how such a set-up came to exist.
These are deep mysteries. At the moment, and probably for ever, they are not accessible to the scientific method. Here religions come into their own, offering answers to riddles about which science chooses to remain mute.
If you want answers, they are available.
Rather a lot of different ones, in fact. Choose whichever one makes you feel most comfortable.
Feeling comfortable, however, is not a criterion recognised by science. It may make us feel warm and fuzzy, but the historical development of scientific understanding shows that, time and again, warm and fuzzy is just a polite way of saying `wrong'.
Belief systems rely on faith, not evidence. They provide answers - but they don't provide any rational process to assess those answers. So although there are questions beyond the capacity of science to answer, that's mostly because science sets itself high standards for evidence, and holds its tongue when there isn't any. The alleged superiority of belief systems compared to science, when it comes to these deep mysteries, stems not from a failure of science, but from the willingness.of belief systems to accept authority without question.
So the religious person can take comfort that his or her beliefs provide answers to deep questions of human existence that are beyond the powers of science, and the atheist can take comfort that there is absolutely no reason to expect those answers to be right. But also no way to prove them wrong, so why don't we just coexist peacefully, stay off each other's turf, and each get on with our own thing? Which is easy to say but harder to do, especially when some people refuse to stick to their own turf, and use political means, or violence, to promote their views, when rational debate long ago demolished them.