(2017-12-10, 12:01 AM)Paul C. Anagnostopoulos Wrote: [ -> ]I note that you keep making up examples: flagellum, rabbit fossil. Do you have any actual examples? I'm not sure how you could have one for irreducible complexity, since it ignores scaffolding. I'm not sure how you could have one for CSI, since it's never been calculated for any biological mechanism.
Concerning irreducible complexity.
"Scaffolding" is supposed to be one of the leading neo-Darwinistic explanations for irreducibly complex biological systems. A biochemical structure is supposed to have functioned as a sort of scaffold of initial additional ultimately unnecessary complexity in the evolution of an IC system before becoming dispensable and disappearing. Sort of a biological analog of the scaffolding needed to build an arch. It would be interesting to see some specific real world examples with complex biological mechanisms, where this argument might actually have some relevance to the real world of biology. I don't think there are any. Natural rock arches and parasites losing unnecessary body parts are not adequate. Another problem with this idea is that it actually adds to the necessary complexity of, and therefore the difficulty of unguided evolution in building, the original system. Scaffolding does nothing to change the fact that the basic function of an irreducibly complex system arises, by definition, only after all the core components of that system are in place. Given a functionally irreducibly complex system whose origin is to be explained by scaffolding, the challenge for the Darwinist is still to identify the sequence of gradual functional intermediaries leading to it.
Exaptation (or co-option from a different use) is another standard orthodox explanation, but it also isn't adequate. The major problem with trying to explain an irreducibly complex system like the bacterial flagellum as a patchwork of co-opted preexisting components originally having different functions is that it requires multiple coordinated co-options. It's not just that one thing evolves for one function, and then, perhaps without any modification at all, gets used for some completely different function. The problem is that multiple protein parts from different functional systems all have to break free and then all have to coalesce to form a newly integrated system (as with an airplane formed by taking parts from a car, bicycle, motorboat, and train).
Even if all the parts (i.e., proteins) for a bacterial flagellum are in place within a cell but serving other functions (extremely unlikely in itself), there is no reason to think that those parts can come together spontaneously to form a tightly integrated system like the flagellum. The problem here is that parts performing functions in separate systems are unlikely to be adapted to each other so that they can work together coherently within a single system. Like a screw formed as part of one subsystem, and a nut formed as part of another subsystem that evolved independently of the first subsystem. It's extremely unlikely that the nut and screw will mechanically work together. This problem is of course much greater in the living cell.
These difficulties are compounded by the need for the simultaneous formation of the assembly system including the instructions for it.
The overall problem with co-option can be summarized in the following. Each of the requirements 1-4 had to have been available simultaneously in the cell. The reader must judge how likely or unlikely this is.
1) All of the component parts must have been present at the same time and in roughly the same place, and all of them must have had other naturally-selectable, alternate useful functions. For the flagellum for example, there is no evidence whatsoever that this ever was the case, or that it ever even could have been the case.
2) The components would have to have been compatible with each other functionally. There is no evidence that this interface compatibility ever existed (between all those imaginary co-opted component parts), or that it even could have existed.
3) An assembly mechanism is required, and that mechanism must be complete in every detail, otherwise incomplete or improper assembly will result, and no naturally-selectable function will be produced.
4) Finally, assembly instructions are required. Assembly must be timed and coordinated properly. And the assembly instructions must be complete in every detail, otherwise no function will result. As noted, the assembly mechanism and the instructions for it are as complicated as the mechanism being assembled, and are also IC.
What is needed is seamless Darwinian accounts that are both detailed and testable of how biological subsystems undergoing "scaffold" formation and removal and coevolution and co-option could gradually transform into irreducibly complex mechanisms, including the assembly mechanisms and instructions. It would be needed to show that it is, at the very least, plausible that a selective advantage could be acquired by the organism at each relatively simple step involving no more than a few mutations at a time (taking into account that more than two coordinated specific mutations at a time are exceedingly unlikely), and identify those steps and the mutations. This hasn't been done yet for the flagellum or any other functionally IC system that I know of.
No such accounts are available or forthcoming. The scientific literature shows a complete absence of detailed, testable, step-by-step proposals for how scaffolding, coevolution and co-option could actually produce irreducibly complex biochemical systems. In place of such proposals, Darwinists simply blithely assert that these general concepts are so compelling that this is how the various functionally IC systems must have come about. I guess we are just supposed to take them at their word.
If such accounts were available, critics of intelligent design would be citing them, and intelligent design would be refuted. Until that happens, such assertions are just statements of faith.