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.

I am greeting you early since I won't be blogging during the holidays. Advice to all workaholics: take some time off!

There's an article in the Sept. 28 issue of Nature discussing the regulation of mating type in two yeast species, c. albicans and s. cerevisiae (regretably, the text is only available if you're on a university network with access to the Nature archives). I'll spare you the gory details, but while the two yeast share the same observable trait (phenotype), the underlying genetic mechanism is completely different.

What is most interesting to me about the article is the detail in which a hypothesis is presented for the evolution of both systems from a common ancestor. The authors list the primary modifications necessary to change one trait into another, note that only a few mutations in one particular protein binding site would be needed to effect one of the modifications, point out that a third yeast species seems to represent an intermediate step between the two, and even suggest future work which includes engineering a strain of s. cerevisiae with the c. albicans mating system, to study what the ancestral yeast might have looked like.

This hypothesis is not only detailed but phenomenally testable (ironically, it involves neutral evolution with no net advantage to the organism). Compare this to the evolutionary arguments for the origin of the bacterial flagella, which rely exclusively on distant (and some not-so-distant) homologies and a good deal of story-telling and hand-waving.

The difference is immediately clear. If all evolutionary inferences were held to the standard of proof present in this nature article, I would have no objections. What I object to is the assumption that natural selection acting on random variation must be sufficiently poweful to fill the gaps between whatever homologies we happen to find in nature.

Can someone give me a good formal definition for intelligence? John McCarthy, a founding father of AI (artificial intelligence) thinks that there does not yet exist a solid definition for intelligence that does not depend on relating it to human intelligence. Here is my proposed informal definition: intelligence is the ability to achieve goals by constraining natural chance processes.

Consider the example of a scantron multiple choice test. Jack totally forgot to study for the test, and so his only recourse was to fill in the blanks at random. Jill, however, studied hard and was able to select the correct answers. We can say that Jill is more intelligent than Jack. While Jack relied totally on chance, Jill was able to curb chance and select the right answers, in order to achieve the goal of getting an A on the test.

So in order to detect artifacts of intelligence, we have to find places in nature where chance was purposefully constrained. This is perhaps where Dembski's explanatory filter comes to play (i.e. if not regularity, then chance; if not chance, then design). We might have to modify the filter a little: if not regularity, then unconstrained chance; if not unconstrained chance, then constrained chance (= design).

Note that intelligence does not need to be the antithesis of chance; rather, intelligence can be the constraining of chance. An intelligent agent can sometimes use constrained chance as a useful tool (e.g. the sorting algorithm known as Quicksort).

We have some catching up to do on this blog! I hope everyone is enjoying the holiday season. As an early Christmas gift, here is a bag of design/evolution links:

• Check out the Time article, God vs. Science (HT: Steve). It's a dialogue between Richard Dawkins, the foremost spokesman for evolution, and Francis Collins, director of the National Human Genome Research Institute. Although Collins is a theistic evolutionist, he does seem to argue for cosmological ID and fine-tuning (see a similar argument in my fine-tuning article).
• New Scientist critically examines Biologic Institute, a lab that is friendly to intelligent design (HT: Evolution News).
• Evolution News has reported that Judge Jones, in the famous Dover intelligent design decision, copied 90% of his section on whether intelligent design is science from an ACLU document. While some skeptics are arguing that this is a widespread legal practice, there is at least one skeptical biochemist who is frowning on this copying.
• Catch a glimpse of some good design with this cell animation from Harvard (HT: TT).