Darwin Unhinged: The Bugs in Evolution

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.

This is all very nice, but aren't we getting ahead of ourselves? Can you name an irreducibly complex biological mechanism that we can focus on?

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).

The flagellum is not IC. Again, can we pick something that is?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1943423/

I won't worry about the rest of your post until we have picked an IC mechanism. But I will come back to it.

Also, could we decide on which definition of IC we're using? For example, is an IC mechanism one which, when reduced, does not maintain its original function or does not have any function? Here are four definitions:

http://www.asa3.org/ASA/education/origins/ic-cr.htm

"Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can't be produced directly, one can't definitively rule out the possibility of an indirect, circuitous route."
---Behe, 1996

~~ Paul