On another thread, betty boop observes that Kauffman speaks of his musings as "proto-science" instead of "science" - that it opens "the conceptual space in which science can (hopefully) fruitfully proceed in the devlopment of its work." Perhaps we can find a good moniker in here somewhere...
One point though, the Intelligent Design theorists do not dispute the age of the universe, the fossil record, or much of evolution theory - and thus would not argue about the evidence for the history of life. The dispute arises over the complexity that all of science and mathematics continues to observe in biological life, i.e. that evolution is not an adequate and/or complete explanation.
And indeed, Darwin's formulation "random mutations + natural selection > species" is no longer adequate because of the "randomness" component. It wouldn't be adequate if there were never such a movement called "Intelligent Design". That part of the investigation will surely continue regardless of format: formal, falsifiable scientific theory, mathematical theory with logical proofs, observation of historical records, proto-science - etc.
Do you mean evolution as a history, or evolution as a specific set of explanations in the realm of molecular biology and game theory? I have no trouble admitting that biology has no complete description of the sources and processes of mutation.
But I do believe that selection is adequate to explain which changes survive. I have been posting this over and over for several days now, but will try one more time. Darwin did not discover anything about the cause or nature of mutation. He really threw up his hands at trying to explain the mechanism of variation.
What Darwin revealed was the process of selection, which shapes life over the long run. Selection is an observable phenomenon. It is amenable to experimentation. In fact it was artificial selection that suggested natural selection.
If you believe there is some miraculous computer program setting up specific changes in the genome -- whether these changes are determined by initial conditions, or twiddled with on the fly -- selection still shapes life. The final arbiter of good design is survival and reproduction. This is true in biology and it is true in the marketplace (where everything is presumably designed, but chaotic and indeterminate forces -- the invisible hand -- shape things in ways that are beyond the control of mere inventors).