As far as examples of how the "millions of years" response is used, actually, I tend to see that in popular science quite regularly.
As PaulK suggests, this is the very opposite of supporting your contention, you are simply reiterating the bare assertion. Plus there is the question of whether 'Popular Science' is representative of the 'scientific community' in any way whatsoever.
I admit to being less well-versed to the world of biochemical evolution, but the responses to Behe's book seemed more diatribe than substance, from a scientific viewpoint.
And again. Please stop just making the same bare assertions. Can you give an example where the 'scientific community' particularly failed to address Behe's argument?
Remember, my interest here is in probability. However, when I have looked at scientific literature the results are mixed. For some macro-scale elements, good results are found, such as the evolution of the eye. The jawed fish is relatively weak. The upright human debate is more speculation than anything else.
What do any of those things have to do with probability? If you think you can make a probability argument based on any of those things you are making exactly the sorts of error you started out talking about. In the absence of a time machine inference is the only tool we can use on these questions. Any probability estimate will surely be the result of extensive inference itself?
However, an objective observer is not satisfied with merely a sparse fossil record to explain complex transitions. (Relatively recent publications re mammalian inner ear tracing do show some exciting lineage, and bear promise to real evolutionary proof rather than inference).
I think you need to explain your thinking here a bit more clearly. What exactly would 'real evolutionary proof' look like? Exactly how would it nor involve inference? When does drawing a connection between fossils stop being a matter of inference? Does extending what we see during the development of extant species to cover extinct species not rely heavily on inference of the genetic basis of the development of extinct species whose genetic makeup is almost universally unknown to us?
I don't believe 'real evolutionary proof' of the sort you ask for can be drawn from the fossil record. Indeed I doubt any probabilistic model based approach could ever provide it. Our 'proofs' such as they are must come from the observations we can make on extant organisms and we have to rely on inference of principles from such research to apply them to what we see in the fossil record.
As to your questions ...
1. How to account for the fact that an existing system can adapt to another purpose, in other words, each feature does not have to evolve from scratch in parallel and independently.
This depends to some extent on whether you wish to retain the original 'purpose' or not. In any case each answer to this question is going to be highly dependent on the actual case. There are a multitude of answers ranging from the loss of need for the original function, the addition of a novel function while retaining the previous function, the duplication of genetic elements allowing the parallel evolution of a separate duplicate system while retaining the function of the original. I would suggest that in most cases it is far easier to explain the development of many traits by co-option and modification of redundant elements of existing systems than by the
de-novo development of such traits. Are you thinking of something specific here?
2. How to model the probability that parallel required system elements will be in place at the required time (the jawed fish example works at the macro scale, but several biochemical system work at the micro scale).
What possible reason would you have to do this? This seems a pointless exercise in the sort of numbers out of a hat navel gazing I thought you were originally objecting to. What 'required time' is there? Are you trying to work out the probability that one particular course of evolutionary history, the one we ourselves are a product of, would occur? Why? What possible value does such a calculation have? The chances are obviously going to be astronomical, but that doesn't make them meaningful, it is exactly like the premise of the tornado in a junkyard argument. or Yockey's essentially meaningless probability estimates for a specific amino acid sequence to appear
de-novo.
3. General Note: The power of the biochemical resources available for evolution is extraordinary. Simple probability which does not recognize the cumulative capabilities of this "system" and its self-organization capabilities can never capture the concept of evolutionary change
And actual evolutionary biologists and geneticists are using it every day in their research, as they were at the time Behe first published 'Darwin's Black Box'. Behe's apparent unfamiliarity with the actual current extant research was one of the major criticisms leveled at the book, i.e. on the evolution of the blood clotting cascade and other supposedly IC systems.
Molecular evolution is perhaps an area where we can think of our inferences as being strongest since they are based on a large body of experimentally derived observations. But even then the estimate of an ancestral gene or protein sequence is still surely just an inference. The probabilities involved surely come from some level of inference inherently like those represented in Bayesian and Maximum-likelihood calculations of phylogeny.
TTFN,
WK
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