Friday, 2 January 2015

The Eubacterial Flagellum - Co-option an Option?

Chapter six of the 2006 book 'Why Intelligent Design Fails' (edited by Matt Young and Taner Edis) is written by Ian Musgrave, a molecular pharmacologist at the University of Adelaide. 

Although his critique of the irreducible complexity of the eubacterial flagellum looks scientifically reasonable at first, a little more research uncovers many significant problems with his rather glib dismissal of the details.

Musgrave notes that the bacterial flagellum is an organelle that looks strikingly similar to a machine constructed by humans. Then, within the same paragraph, he contradicts this assertion with the claim that: '..."the" bacterial flagellum does not exist'. One cannot help feeling that this irrational conclusion is partly motivated by a rejection of learning. What could he possibly mean by this blatant contradiction? It seems that in an attempt to think comparatively, Musgrave is also trying to draw our attention away from the object of cognitive conflict (the eubacterial flagellum), and introduce other types of flagella (e.g. Archaeal flagella). Yet significantly, he fails here to note that these other flagella (including their basal bodies) are by no means plausible intermediates, but totally distinct systems - fundamentally different in many respects from the eubacterial propeller.

William Dembski finds models of the evolution of the eubacterial flagellum unconvincing. Yet Musgrave claims that: '...[Dembski] does not seem to understand that the eubacterial flagellum is only one of a range of motility systems in bacteria...and that motility is just one function of the flagellum.' This is clear equivocation. Many flagellum experts [including Professor Scott Minnich] understand very well that there are other motility systems designed for life at a low Reynolds number. Yet all of these systems (except type-III secretory systems) share no significant homologies with the bacterial flagellum, and therefore cannot contribute to a hypothetical Darwinian pathway. Furthermore, while it is true that the eubacterial flagellum does contain a sub-system that superficially resembles a Type III secretory system, this flagellar subsystem is a vital engineering solution which allows assembly to occur from the bottom of the filament up. Therefore, half-baked attempts to impose a historical interpretation are utterly unjustified.

However, Musgrave continues this critique by suggesting: 'The flagellum is probably not IC at all because the original function of the eubacterial flagellum, which can survive massive pruning of its components, is almost certainly secretion, not motility'. This reasoning is severely flawed. It is somewhat equivalent, upon spying a light aircraft, to claiming that the original function of the aircraft - which can survive massive pruning of its wings, tail flaps etc. - is almost certainly road transport, not flight. Indeed, comparative analysis with both a Reliant Robin and a Sinclair C5 shows that all light aircraft probably arose through co-option and simple modification of a three wheeled precursor which perhaps originally functioned as a lawnmower. Clearly when we see design we can always rationalize it away with a historical just-so story, but such stories become highly implausible.

This chapter next presents evidence for homologies with the Type III secretory system. Here, the extent of homology with this system is quite overblown. The Type III secretory system contains no homologues for a number of vital components including MotA, MotB, FliM, FliE, and possibly FliO and the filament forming chaperone FliD. In addition:

1. The type III homologue of FliN only shares sequence similarity in 80 C-terminal amino acids.

2. The similarity between FliG homologs is very poor indeed.

3. The FliF homologue in the Type III secretory system has both the C- and N-terminal domains missing and is probably incapable of substituting for flagellar FliF.

Most models also assume the existence of the Type III secretory system to begin with. Yet the origin of this system is far from clear. Some scientists have recently suggested that it could have been coopted from an already functioning ATP synthase. Yet this is simply clutching at straws because there are many dissimilarities between these systems and the origin of ATP synthase as a ubiquitous system is itself equally obscure. Primitive ATP synthases are simply non-existent.

Analysing this a little deeper reveals that the Type III secretory system is not the proposed Darwinian intermediate for the eubacterial flagellum anyway. What, according to Musgrave, is then? The final answer - it turns out - is a 'general, ancestral type-III system' which cannot be identified but must simply be imagined! No surprises there then! In fact, what we have here is a molecular 'missing link'. Perhaps we can anticipate the next logical step for evolutionary molecular biology: a theory of punctuated equilibrium for molecular systems!

After arguing that the eubacterial flagella performs many other functions - including secretion - Musgrave suggests: 'Secretion plays a crutial role in this organelle, so you can't make flagella without secretion, so secretion must be the original function.' This is very questionable reasoning indeed. What it totally ignores is the remarkable, systematic, assembly order of this organelle.

It turns out that when the eubacterial flagellum is assembled, the rotor housing (FliF) forms first, followed by the rotor/switch (FliG,M,N), followed by the protein export apparatus (FlhA,B,FliO,P,Q,R), followed by the motor proteins (MotA,B); then the rod, the secretory P and L rings, and finally the hook, junction, cap and filament. The implications of this sequence are very significant. Since the assembly sequence which is most plausible from a historical perspective is quite dissimilar to the actual assembly sequence, something is clearly wrong with Musgrave's model. In all evolutionary models, the export and secretory systems are always assumed very early on. In reality, however, the switch complex must be formed first in order to incorporate the export apparatus. Since the switch and rotor only function as part of the rotary flagellum system, the rotary propeller function of the flagellum is implicit from the beginning - a clear case of "teleological assembly".

Teleological assembly doesn't stop there, however. Evolutionary models (assuming Gram-negative origins) also suggest a secretin is formed in the peptidoglycan and lipopolysaccharide wall layers  - before the rod complex. This is in order to provide a hollow tube for surface adhesins to oligomerize (without a chaperone!) to form an adhesive proto-pilus. However, in order to oligomerize and puncture the two wall layers, the rod complex (FliE, FlgB, FlgC/F and FlgG) in the eubacterial flagellum actually seems to drill through the walls using the proton-motive force of the motor proteins. The motor proteins are therefore incorporated before the rod pierces through the two layers, and the P and L secretory rings are only incorporated as the rod penetrates each layer of the wall respectively. Needless to say, this assembly sequence is extremely counter-intuitive from an evolutionary perspective. Yet teleologic assembly makes perfect sense within a paradigm of intelligent design.

In closing, Musgrave concludes: 'Being IC does not eliminate indirect evolutionary explanations, and flagella can evolve from simpler systems through a series of functional intermediates.' Yet nowhere has Musgrave actually demonstrated a scientifically plausible, non-direct Darwinian pathway, and nowhere has he provided any plausible intermediates with significant homology to the eubacterial flagellum.

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