Kitzmiller, the Universe, and Everything

It is exactly the opposite! All designed things do not necessarily have high FI, but things with high FI are designed.

But isn’t it expected to observe a higher score between two fishes of the same family (cyprinid) than between a fish of that family and a mammal. I am pretty sure that the bitscores for Astrotactin 2 between 2 mammals, say human and mouse, would be higher than between human and the winnow? According to gpuccio, the higher divergence observed between cyprinid fishes and mammals has 2 possible components;

  1. divergence due to neutral variation and drift
  2. divergence due to different functional specificities in the 2 types of organisms. Gpuccio calls this type of divergence « functional divergence »

Now, there is one thing I found surprising with the scores I reported in my post, ie., they are higher in lizards, birds and mammals than in amphibians. I would have expected the opposite.

He said it can be shown that genes demonstrably do arise(which it can), not that we can travel back in time to see how some particular extant gene evolved in the ancient past.

Nevertheless, there is actually good evidence for how the alpha and beta chains of ATP synthase evolved. They evolved and diverged by gene-duplication of a common ancestral protein functionally and structurally similar to both. In some related structures such as hexameric helicases, it is the same protein oligomerized six times, instead of two similar duplicates(alpha and beta) three times.

There’s a nice phylogenetic tree of the related proteins in both F-type and V-type ATP-synthases, and other P-loop NTPase proteins, in this paper:
Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV. Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nat Rev Microbiol. 2007 Nov;5(11):892-9. Review. DOI:10.1038/nrmicro1767

Click to enlarge.

Key question: Why should this evidence exist? If these proteins did not evolve from common ancestors with different related functions, why can we detect high levels of nesting hierarchical structure in their shared similar sequences? Why do they all form catalytic hexamers that implement their functions by ATP binding and hydrolysis?

And hey, I have another post written 21 days ago in direct response to you on the inferred origin of P-loop NTPases. On a related subject, one of those papers on de novo evolved proteins I’ve shown here before many times describes a randomly generated peptide that gives antibiotic resistance to bacteria. Turns out the peptide forms a membrane proton channel.


Ah, very good.

So let’s apply that:

A red Porsche is red, therefore it was designed.

A red apple is red, so it was designed.

Rust is red, so it was designed.


I somehow find that something is missing from that argument,

Are you saying that Dembski had a mathematical proof? I have not found any that is valid. Anyway, what you want to talk about is Behe’s arguments. There I yield to the other commenters here, who have done a great job of pointing out why those don’t work.

I think Dembski and the group in Texas are working on a mathematical proof which you and Tom are providing feedback for.

As far a Behe’s work goes I see this discussion continuing for some time until a mechanism can be shown to produce the complex macro machines that are pointed out in the paper that Rum cited.

The more recent the common ancestor (or, more properly, the longer the path through the tree), the higher the scores should be. The issue of it being “the same family” is not a good way to predict, Humans erect families in very biased ways. For example, the genus Drosophila is about 50 million years old. Things that don’t look like us get lumped into large groups, while mammals get split much more finely. The phylogeny is not subject to that bias.

And in any case, we’re comparing everything to the pinnacle of creation, the minnow, not two mammals to each other. The high Blast score of two cyprinids is then supposed to convince us that they have accumulated a bunch more “information”.

I would have expected those to be about equal, as the common ancestor of lizards with cyprinid fishes is also the common ancestor of amphibians with cyprinid fishes. But if molecular evolution is not perfectly clocklike, then those two numbers could differ – in this case faster evolution in amphibians could do that.

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Well, I had a whole post at Panda’s Thumb pointing out that the criterion they are using (Algorithmic Specified Complexity) had nothing to do with showing whether natural selection could bring about adaptations. Instead it talks about how short a computer program can compute how long a bitstring. They somehow think that this tells us something, and they want to provide a mathematical proof that this quantity is conserved. And when asked how that quantity tells us anything about adaptation, they say that well, we’re not biologists. And Tom has provided counterexamples to their assertion of conservation. So they’re dead in the water on two counts. But obviously you expect great things from their effort. I wouldn’t hold my breath if I were you.


If we for relative comparisons were to say insulin at 50AA’s and 150 nucleotides was a smaller step then a flagellar with 30000 AA’s and 100000 nucleotides? Both of these are a challenge for the Darwinian mechanism but I would claim that the flagellar is a bigger challenge.

I don’t see any empirical data so far eliminating their Idea from consideration. I do see mathematical inconsistencies that Tom has pointed out. Do you think this discussion is really dead?

You have not one bit of evidence for that assertion. We have plenty of evidence it’s not true. Attempts to define ID-Creation into existence are pretty silly.


Their argument was not an empirical one but claimed to involve a proof (originally it was the Law of Conservation of Complex Specified Information). That claim of a theoretical proof that natural selection can’t in principle get you to higher adaptation is extremely dead, seriously dead. I’m sorry sir, but your parrot is dead. But it walks the earth at night with glowing eyes, when the full moon is out. At least it does when Eric Holloway goes around declaring that no one has given any sensible refutation of Dembski’s arguments. And it does in your statements too.


FFS Bill there’s no such thing as a flagellar. It’s a flagellum (singular), flagella (plural). Flagellar is an adjective. You can’t be bothered to even learn simple terminology then you wonder why people don’t take your whining seriously.

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The mechanism is known Bill. It’s called evolution. Sigh.

Where is your model that shows an algorithmic generation of a sequence such as the English language that does not contain the sequence itself? I have spent some time with Weasel. Although I agree there are holes in their proof that you have shown you have not defeated their concept until you can show algorithmic generation of information.

Eric’s most interesting point is this concept (algorithmic generation of information) is defeated by the Turing halting problem.

Note that Bill has had his demand answered numerous times before, like by this experiment with evolving soft bodied robots. There was no target, no pre-determined sequence. The only broad “goal” was to outperform your neighbors.

For some unknown reason Bill thinks denying scientific evidence is the way to go about supporting his belief in the Christian God. It’s very strange.

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That’s quite an oversimplification. The flagellum isn’t one big protein 30.000 amino acids long, rather it is composed of many smaller proteins. So to evolve a flagellum gradually we’d have to come up with a model for how adding proteins to simpler versions lacking these proteins, could yield a function. There is evidence for this.
Many of those proteins are homologous, they derive from common ancestors. There are structures similar to the flagellum, that lack different versions of these proteins, which nevertheless also function as flagella. There are more distantly related versions of flagella-like structures that have other functions besides motility, such as membrane channels and secretion systems, bacterial pili, and surface adhesion systems.

So to give an evolutionary account for the origin and evolution of some bacterial flagellum, you’d show that there is a plausible route where the present system could evolve incrementally from simpler systems that show evidence of being related to the flagellum, yet retain useful functions throughout. That was done by Nick Matzke in 2003 in the article linked above.

Sure those are challenges put forward by critics of evolution such as Michael Behe, and I also agree that an entire multi-component flagellum as a larger and more complex system is a bigger challenge than a single protein. I don’t think any reasonable person would dispute that. It’s just that I think that challenge has been overcome. There is a very good in principle account of how such complex structures can grown incrementally while having different useful functions throughout, and there is good phylogenetic evidence for the different stages in the evolution of the structure in question, from comparative molecular biology and genetics.

It is important to remember that the model for the evolution of the flagellum does not posit any mechanisms that have not been observed before. It involves mundane things like the different types of mutations: substitutions, insertions/deletions, duplications, and then having these mutations be subject to natural selection.

That is completely standard scientific reasoning about past events given processes observed in the present, just as geologists do about plate tectonics and mountains, and astrophysicists do about gravity, stars, and planets.
Presently observed mechanisms are postulated to have occurred in the past in very specific and particular ways that may seem a priori unlikely, to account for very specific extant objects, such as a specific mountain range or single specific mountain, or the precise and specific pattern of craters on the moon.

In that same way, presently observed mechanisms are invoked to explain how there were long series of historical events that resulted in some particular molecular structure in reproducing cells.


Good example of why colewd’s argument is wrong. Another excellent example is BoxCar2D, which evolves creatures that move to the right, without ever having any design for them present, nothing except assessment of how far they have moved in that direction. (That page seems to require a recent version of Adobe Flash, alas). I’m sorry, your parrot is quite dead.

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Sadly Bill is quite impervious to all scientific evidence. He’s decided his Christian God (which he refers to as a disembodied mind) had to magically POOF all life into existence. Any and all evidence for natural processes like evolution are wrong by definition.

Bill is a classic example of the old adage you can’t reason a man out of a position he wasn’t reasoned into in the first place.


This is where we disagree. I don’t think Matzke’s paper gets to 9th inning of solving the problem but maybe to the bottom of the second.

The argument here is that we are arguing design vs natural known mechanisms. If for arguments sake you concede that some of biology is designed does that change your view of the origin of the flagellum.