But in the issue of the ATP synthase, the TTSS, and the bacterial flagellum, the evolutionary scenario doesn't appear to be nearly as plausible. And if the similar proteins perform similar functions in all three systems, it could be common design is involved. But again, I'm talking about systems I don't fully understand, so I'm not trying to argue dogmatically for common design. Just wondering if it would explain things in this case.

IC is not ID, Nick.

Hmmm…

ID=religion
IC=ID
therefore
IC=religion

Should mousetraps be considered sacred relics then?

You used IC to argue against the hypothesized homology between the two systems.

IC is not ID, Nick. I have yet to make an ID case. All in good time.

You may as well get started, as the flagellum does not appear until volume 2.

However, I don't think nested hierarchies by themselves should be the sole determinant of common descent. We would also want some plausible evolutionary pathway from one to the other. And if the functions of the proteins in the three systems are similar, it may be that they were chosen because they are optimal for those kinds of systems.

Bilbo,

Nobody is arguing that a nested hierarchy based on a single character is decisive evidence for common descent. But when you look at character after character, both molecular and morphological, and they all yield congruent hierarchies, then the odds that this is not due to common descent are infinitesimal — unless, as I said before, the designer chose to make life appear as if common descent had taken place.

Common design predicts that hierarchies based on different characters need not be congruent. Common descent predicts that they will be. Common descent is overwhelmingly confirmed.

See Douglas Theobald's excellent online summary of this here.

I have been planning on writing this up in simpler terminology, but I am waiting for what Mike Gene says in his book!

Nick

Essentially the flagellum/F1F0-ATPase homology idea is that *inside* the rotating base of the flagellum, the inner proteins that form the secretion machinery (aka "Type 3 Secretion") are homologous to the F1F0-ATPase. This might mean that the flagellum has two rotary motors, one inside the other.

(Although I wouldn't bet on it. For various reasons it looks to me like export/secretion might be the ancestral function, and the rotation and linkage of proton pumping to ATP are traits that were derived in the line leading to the F1F0-ATPase and its relatives. The duplication that produced the alpha/beta subunits is already known to be derived.)

(Note that the previous paragraph was not an idea present in the 2003 Big Flagellum Essay.)

in general there is a simple criterion for distinguishing common design from common descent. Common descent forms nested hierarchies. Common design does not , unless the designer deliberately chooses to make it appear as if common descent had happened.

I'm not sure how far I should pursue this, since — for all I know — it may have nothing to do with the current example of homologous proteins between the ATP synthase, the TTSS, and the bacterial flagellum. However, I don't think nested hierarchies by themselves should be the sole determinant of common descent. We would also want some plausible evolutionary pathway from one to the other. And if the functions of the proteins in the three systems are similar, it may be that they were chosen because they are optimal for those kinds of systems. But again, I'm speaking out of ignorance here. So if Nick or some other critic wants to slap me down, just be gentle.

My own "” and no doubt "” very simplistic view, is that since all three systems depend upon a wheel in order to work, it wouldn't surprise my if a designer decided to use similar parts for the wheel in all three systems.

Hi Bilbo,

I'm not familiar with the specifics of ATP synthase or the TTSS, but in general there is a simple criterion for distinguishing common design from common descent. Common descent forms nested hierarchies. Common design does not , unless the designer deliberately chooses to make it appear as if common descent had happened.