Posted: Jul 22, 2010 1:57 pm
by Rumraket
CharlieM wrote:One thing I don't want to do is get into a Monty Python type argument about IC and things seem to be heading that way. That is why I would prefer to get into more detail and I'm concentrating on the flagellar hook because I see this as possibly the strongest position to argue for the IC of the flagellum. So if anyone can convince me that this is easily explained by unguided natural means, I'm ready to listen.

There is a problem with just saying it has homologs and that's it. Here is a link and an excerpts so that you can see some of the difficulties. It explains one domain of a single hook protein:

D1 has a rather complex, unusual fold composed of many different folding motifs: a stack of four horizontal b-hairpins one above another, alternating their orientations with crossing angles of about 1208 (Asn 79–Leu 115 and Gly 324–Gln 337, on the left side in Fig. 1); a triangular loop (Thr 116–Pro 135, on the right side in front); a four-stranded (Leu 288–Ile 314 and Asn 357–Ser 363) and a two-stranded (Val 315–Asn 321 and Ser 339–Thr 346) b-sheet (in the upper and lower half, respectively, both on the back side); two consecutive b-turns (Thr 346–Phe 352, behind the triangular loop); and a vertically extended chain (Pro 135–Ala 144, in the centre front of the upper half). This extended chain seems to be a backbone around which the other motifs assemble. A three-dimensional structural similarity search using software DALI25 resulted in no match for domain D1, confirming its unique fold. The longest dimensions of domain D1 and D2 are about 50 and 45A ° , respectively, and these two domains are connected along their long axes with an angle of about 708.

As predicted from amino acid sequences and expected from farultraviolet circular dichroic spectra, the structure of FlgE31 is very different from that of the F41 fragment of flagellin21,26, which consists of three domains with domain D1, which consists of three a-helices and a b-hairpin, domain D2, which is formed from many b-hairpins, and domain D3, which is made of a tight b-barrel. It is curious that these two molecules with completely different structures both form the tubular structures with basically the same architecture and helical symmetry.

Well to be honest I don't even think the evolution of the hook poses much of a problem and a possible solution is quite simple.
What I'm going to detail here is just my personal layman's(inspired by Matzke's account and CDK007's video on youtube) take on the issue and please don't confuse my uneducated ramblings with those of possibly much more competent evolutionary biologists.

In any case, look at it this way : To begin with, what later became the hook was simply a duplicated gene of the rod protein making gene, which itself is is an evolved adhesion protein secreted by secretion apparatus. (Notice how the proteins making up the pilus, the later filament and the hook, are all homogous to each other. Additionally they are mutated duplications of adhesion proteins; a sticky substance that likes to "stick together". It propably doesn't take many mutations in such a protein to make it more structurally rigid. A perfect candidate for evolving various structural components with elasticity or similar useful traits).

This duplicated rod is straight to begin with and is slowly accumulating mutations making it bend while retaining structure. Remember, these are individual molecules sticking together entirely by intermolecular attraction forces. It is not unreasonable to postulate that this complex can undergo a very slight twist without breaking. And the proto-flagellum was propably quite slowly rotating. What is now left for evolution to do is simply to filther through mutations for improved function over generations. The pro-flagellum before a bent hook as we see it today arrived, was providing motility already, but it was poor at it. But poor is better than none at all.

A mutation happens in the proto-hook allowing it to bend slightly more, without breaking. Through generations of accumulating mutations the hook we see today becomes a reality and along this path of evolutionary history are mutations in the filament genes for increased function. Mutations in the Tol-Pal proton motion machine for increased function in its association with the rod. The rod is accumulating mutations for increased strength. None of these postulates are unreasonable in any way. The entire flagellum didn't have to assemble in one huge step. Minor adaptation on duplications yielding ever increased function over generations.

Before it was a motility flagellum, it was an adhesion protein secreting apparatus. The adhesion secretion apparatus evolved superior function and at some point, the secretion system was providing poor motility. And poor was better than none at all.