I've said before that the standards of proof which design theorists require for an evolutionary inference is wildly different from the standard accepted (and usually given) by evolutionists. I've just read a new paper by Pallen and Matzke, From the Origin of Species to the origin of bacterial flagella, and it perfectly illustrates the disconnect. My comments on some quotes from the paper:

By even the most conservative estimate, there must therefore be thousands of different bacterial flagellar systems, perhaps even millions... either there were thousands or even millions of individual creation events, which strains Occam's razor to the breaking point, or one has to accept that all the highly diverse contemporary flagellar systems have evolved from a common ancestor.

First of all, this is rather sloppy use of Occam's razor. All things being equal, a simpler explanation should be prefered to a more complex one. But are all things equal? That is the interesting question. Pallen & Matzke gloss over it, assuming the truth of the controversial premise. This is blatant begging of the question.

Secondly, I don't know if all bacterial flagella descended from a single ancestor by a process of natural selection acting on random variation. They may have. But it takes more than common ancestry, inferred from protein sequence similarities, to decide the question. Common ancestry in itself says nothing about the processes acting on the (simpler?) ancestral flagella which caused it to resemble a modern one over time - only that it did.

What would it take to establish such an evolutionary hypothesis? Real evidence (as opposed to inference from historical data based on naturalistic assumptions) that natural selection is capable of doing that sort of thing.

Thirdly, Pallen & Matzke are clearly relying on a theoretical principle rather than experimental data for the force of their argument. It is fairly obvious that they do not consider creation an allowable explanation. This is fine and good so long as the principle is subservient to the data. But principles can be wrong. They have been wrong. For example: at the beginning of the last century, almost all physicists believed in an infinite, steady-state universe. The concept of a universe with a finite age was actually repugnant to many of them, on purely philosophical grounds. When the Big-Bang theory was first proposed (by a Christian, incidentally - someone with a prior commitment to a creation event) it was opposed for that reason for quite a while before the evidence overwhelmed the sceptics. I wonder if the same thing is in the process of happening in biology.

...but if one accepts that all current flagellar systems diverged from their last common ancestor (the ur-flagellum), why stop there? All flagellins show sequence similarity indicitave of common ancestry... Therefore [on the basis of homology with non-flagellar proteins] the flagellar rod-hook-filament complex has clearly evolved by multiple rounds of gene duplication and subsequent diversification.

I really don't know what to say to this. If protein homology is all the proof of darwinian evolution that you needed, then we should shut down this blog and go home. But it seems clear to me that it is not. Citing homologies does no prove what Pallen & Matzke seem to think it does.

From the above discussions of sequence hommologies and modularity, it is clear that designing an evolutionary model to account for the origin of the bacterial flagella requires no great coneptual leap.

As I have argued before, the hand-waving about homology and possible precursor systems does not approach the level of detail needed to convince anyone familiar with the implementation of complex systems that it is as simple as it sounds.

the flagellar research community has scarcely begun to consider how these systems have evolved. This neglect probably stems from a reluctance to engage in the 'armchair speculation' inherent in building evolutionary models
....
it is no longer enough to say, for example, that bacterial flagella evolved and that is that. Instead, scientific experts have to engage with a sceptical public.