I would submit, as a preliminary, that there has been no Darwinian progress on explaining molecular machinery and that all of the stuff that has been alluded to and much more is actually just regular biochemistry, which is being spun in a Darwinian fashion. Let me start with the bacterial flagellum and the type 3 secretory system- the idea which has been popularized by Ken Miller – is that perhaps this type 3 secretory system, which is actually just a little injection apparatus, could have been a precursor to the bacterial flagellum, which is in fact a rotary motor. To get across the problem with that, I’m going to start with a cartoon example that I started with, and Ken Miller picked up on. I started to illustrate the idea of irreducible complexity. I used a mouse trap and I think probably many people in the audience are familiar with that. A mousetrap has a number of different parts and all of the parts are necessary. In a number of different venues, Ken has said “You can use the mouse trap for other things, you can use it for a clipboard, you can remove pieces and use it as a keychain, you can even use part of it as a paperweight.” It sounds pretty good when he says that but when you see pictures of real clipboards and keychains and paperweights, somehow the idea is the paperweight would be used to make a keychain, which would be used to make a clipboard, this would somehow end up as a mouse trap? Darwinists want you to think that making transitions is easy, let’s just start with a paper weight, and then we can go to a keychain, so it’s not irreducible.
The only thing is that going from a paper weight to a keychain is not the same as going from a gene for one function to another with maybe five mutations are sufficient.
I would consider this an intellectually unserious response to the problem of irreducible complexity. Another problem is that if you start with some structure that’s being selected to be a paperweight, it’s not going to be prepared at all to be a keychain. A structure that’s a keychain isn’t going to be prepared at all for a clipboard. If somebody says “I’m going to accept this and use it for a clipboard”, you might as well say “I’m going to accept a paperweight”. You haven’t gone any of the way towards a clipboard.
Michael, what about the question I asked. Suppose you have an irreducibly complex molecular machine made up of six different parts labeled “A” to “F”. Suppose that they started out as individual precursors, each of which had their own function. Suppose they got together and somehow now you could have an irreducibly complex machine. But each of the parts had their own function and even if all of these things are doing the exact same thing they would do in the irreducibly complex machine, you still can’t get from these parts to here. Because proteins are not little colored squares. Why does the “A” go next to the “B” here? Why doesn’t it go down here? Why aren’t these in a line instead of something like this? What makes a real protein stick to another real protein? They stick to each other because they have very complex surfaces which are matched to each other. The chemical and physical properties have to be just so, like little magnets that are lined up, in order to allow them to bind. This is the real problem that would face that scenario. You would have proteins A B C D, which did not have the right shapes. In order to bind to each other, in order to form an irreducibly complex molecular machine, they would have to pre-adapt all of their shapes in order just to bind to each other.