My commentary on John Bracht's posting begins in the middle since I have nothing to say about coin-flipping machines.  I do, however, have something to say about molecular evolution.

To start with, in his article, Bracht says:

"Now take these ideas into the realm of biology.  Consider the intensively studied bacterial flagellum [2]," where note 2 reads "See, for instance, Michael Behe, Darwin's Black Box (New York: Simon &Schuster, 1996), 70-72 and William Dembski, Chapter 5 of No Free Lunch.”  It would behoove Mr. Bracht to someday read, or at least cite, the original literature on these organelles (e.g. Howard Berg, David DeRosier) rather than citing Behe and Dembski as in ref. 2.

Moreover, according to Bracht:

"This complex biological structure is a micro-scale molecular motor that the bacterium uses to propel itself through its environment.  It consists of an acid-powered engine, a drive shaft, U-joint, stator, rotor rings, and propeller.  It is a highly integrated system that requires each of fifty or so different proteins in order to assemble properly and function.  Furthermore, there are many bacteria that entirely lack a flagellum and are nonmotile, and they survive and reproduce perfectly well.  Thus, while there may be a fitness benefit to having a flagellum, there seems to be no universal drive to acquire a flagellum since not all bacteria have one.  This is a key distinction between biological organisms and Young's machines that inevitably produce the sequence favored by the pre-selected fitness function.  Natural selection operates in a very different way than the fitness functions of the coin-flipping machines because it does not have a predetermined outcome.  The complexities of the real-world fitness function are dependent on the environment and are difficult to conceptualize in a concrete way.  However, it is abundantly clear that there is no pre-determination as in Young's coin-flipping machines.  Furthermore, experiments and theory suggest that the flagellum is targeted by a sheer, sudden mountain or plateau rising from a flat plain-the sort of fitness function that is not explored well by evolutionary processes."

 He goes on to say:

"In order for the fitness function to have smoothly sloped sides rather than sharp cliffs, there must be a way to gradually build a flagellum with fitness increases at each step as parts of the system are added.  It is common for biologists to do mutation experiments in which they destroy some component of a molecular system and see whether it still works; with the flagellum they have found that all the components are required for function.  In other words, the intermediates are non-functional and thus convey no selective advantage."

 This is the critical moment in the ID/Behe argument that biologists have been blowing a whistle at for years, to no apparent avail.  I will once again blow the whistle.

The fact that the modern components of the modern bacterial flagellum are required for function -- mutations in any component destroy function -- says nothing about the original properties of the intermediates.  A protein originally "added to" a primal flagellum (the precursor to protein #18 of the modern flagellum, let's say) does not need to be posited as having been necessary to primal flagellar function at all.  Its mutation-conferred chance ability to associate with the primal flagellum would by definition be an "extra," since the primal flagellum had, by definition, some sort of a functionality on its own or we wouldn't call it a flagellum.  All we need to posit is that when the original version of #18 added on, the primal flagellum worked better in some way, the creature was "fitter," natural selection operated, and the gene spread.

Now enter a process abundantly documented in the biological literature but ignored in ID arguments with which I am familiar, namely, the process of co-evolution.  If our protein #18 initially conferred its freebie advantage by binding to pre-existing protein #9, let's say, then what happens during co-evolution is that any mutations in protein #9 that permit #18 to bind better, or better confer its selectable advantage, are also going to spread, as will any mutations in #18 that permit #9 to better bind to it or help it in its function.  It's like in an electronic device that an engineer realizes can be improved by adding a new gizmo.  At first the gizmo is an "attachment" -- the device works fine without it and the gizmo may well have a life of its own as well -- but then the engineer realizes that if she makes this and that change to the device and this and that change to the gizmo, the gizmo becomes integral to the overall circuitry and the machine works even better as a result.  Not unexpectedly, this new-and-improved machine doesn't work if there are malfunctions in either the gizmo-derived component or the machine-derived component of this now-integrated unit, just as, and in the same way as, the new flagellum no longer works if either #9 or #18 are rendered inoperant by mutation.  The two, having co-evolved, have become co-dependent where they were once independent.  It is not necessary to posit that there was no machine at all until all its present-day components were in place just because they are now all necessary for function, and it is not necessary to posit that there was no flagellum at all until all its present-day components were in place just because they are now all necessary for function.

For instance, Bracht observes:

"In contrast to the coin-flipping machines in which a sequence has progressively greater selective value the more heads it contains, there is no advantage in having a nearly complete flagellum."

Who says the present-day flagellum is complete?  Why in another billion years, if there's still planetary life at all, bacteria may have flagella that make the ones around now look like Model T's, with all sorts of new dedicated gizmos which, if knocked out by mutation, disallow overall function.  And likewise, the very first flagellum might have been nothing more than a rotating ATPase (found throughout the biological kingdom) with some fibrous protein (independently a cell-wall component or some such) attached to it.  Sounds "complete" enough to move you through the water a bit more than if you didn't have one, and adaptive enough to be a substrate for natural selection.  And if you were a biologist around at that time studying bacteria and came upon this motility device, you might well have dubbed it "complete," not knowing of the 50-polypeptide unit that lay ahead.

Here is another point of Bracht's: "The system doesn't function until all the parts are assembled, so selection cannot preserve the intermediates and work gradually toward the flagellum."

This is an invalid assumption, for the lack of function for intermediates means that the functioning flagellum is the only high point on the fitness landscape; the surrounding terrain is flat and uninformative to the selection process.  Only chance, stumbling upon the flagellum unaided, is capable of generating the flagellum.  In such a situation, we can assess the probability of chance putting all the pieces together, and the probability is far below what is reasonable to occur even once in the entire history of the universe.  Thus, design theorists claim that the bacterial flagellum is beyond the reach of chance and law.

Bracht then adds that

"Many will accuse me of misrepresenting the Darwinian process.  The flagellum wasn't produced purely by chance.  Rather, the components were pre-existing in the cell and were co-opted to form the flagellum at some point in the past.  To get around the improbabilities of a pure chance assembly of the flagellum system-a scenario all Darwinists reject as simply too improbable-the co-optation model hypothesizes that all the proteins were already present and performing different (non-flagellum) functions in the cell and evolution utilized these pre-existing components to cobble together the flagellum.  However, this model actually makes it more difficult to generate the flagellum because it postulates that all the requisite proteins were adapted to other functions prior to being incorporated into the flagellum.  This implies that the proteins would require extensive revision before they would be properly suited to work together in the novel flagellum.  Furthermore, the fact that all fifty proteins are crucial for the function of the flagellum implies that the proteins must all have shifted their structure and function at the same time to come together into the new flagellum system-and this shift somehow did not disrupt any essential cellular process previously performed by these proteins.  By hypothesizing that precursors to flagellum proteins had their own specialized functions the co-optation model creates a very large gap between the old system(s) and the new system-a gap that must be crossed in one step to maintain selectable function.  It is this sudden, coordinated shift in protein function that is the major problem with the co-optation hypothesis.  The beauty of Darwin's theory was that it replaced miracle with mechanism and gave a law-like account of how the species developed.  But here we see that the Darwinian explanation of the bacterial flagellum replaces mechanism with miracle, a collective shrug and vague gesture toward a chance macromutation that modified and brought the components together in one fell swoop.  The co-optation model doesn't alleviate the improbability of the flagellum's origin; it actually embraces an enormous leap of chance as a key element of the scenario."

And yet I repeat.  All of the above is predicated on the notion that the flagellum must have happened in one fell swoop, that you either had no flagellum or one with 50 essential proteins previously engaged in other functions, which is indeed silly.  This house of cards, however, is constructed on the observation that you have to have all 50 for the modern flagellum to function.  If you allow as how the original flagellum might have consisted of 2 proteins, and factor in the co-evolution of dependency once new components are added, then the house of cards collapses.

By way of illustrating his point, Brach writes the following:

"For concreteness, consider an example.  Think of a man-made outboard motor.  This system contains many of the same structures found in the bacterial flagellum: a motor (including stator, rotor, and acid-powered drive), drive shaft, u-joint, and propeller.  Now, imagine starting with a basic rowboat and trying to evolve an outboard motor via the co-optation model.  Perhaps, somehow, the metal outer skin of the boat peels up in the back and this forms a useful rack for a fishing pole, and is available to provide the internal support and external protective casing for the motor.  Perhaps a support rod works loose from the hull and is available to be made into a drive shaft.  But how do we move on from here to build up the motor, in functional steps, from existing parts?  The problem is this: the various parts are already adapted to their old functions.  To build an outboard motor, the old functions must be replaced by new functions.  New functions require modifications of the old parts, and since the motor system doesn't work until all the parts are assembled."

This, too, is an invalid assumption, about which I will elaborate below; but Mr. Bracht continues by saying.

"...we inevitably need a large amount of coordinated change in various components before we can build the new system.  For instance, the peeled-away metal on the back (previously adapted to form a watertight hull) will have to undergo extensive modification, including careful bending or shaping, and drilling holes in appropriate places to support motor components (all without letting the hull become leaky).  The support rod from the hull, destined to become the drive shaft, will also need modification for attaching gears and the universal joint (and the removal of the support rod must not weaken the structural integrity of the boat).  And so on."

While this is an imaginative extrapolation from mousetrap to motor, but the problems with the analogy remain, since Mr. Bracht seems to think that all these events have to occur simultaneously, the phenomenon of gene duplication has no place in his arguments.  But since the phenomenon is commonly omitted from other ID arguments as well, let me point out that once one realizes that it is not necessary to build the flagellum in one fell swoop, it is also helpful to realize that it is also not necessary to take a protein that performs one function and immediately "co-opt" it so that it performs a second, flagellum-related function.  The many genomic sequences now available offer numerous instances of gene duplication wherein a gene duplicates, the original function is "covered" by one copy, and the second copy can go on to accumulate mutations and, perhaps, by chance, come to encode a novel protein with some novel adaptive function.  So, the gene encoding our fibrous protein that forms part of the cell wall might have duplicated and one copy might have accumulated mutations that allowed its protein product to bind to the outside of a rotating ATPase and become the first biological propeller."

In his conclusion, Bracht begins by saying:

"The bottom line is that there is no smooth gradient leading to a functioning outboard motor...."

Sure there is! For example,

Wheel --> water wheel --> ox-driven water wheel --> internal-combustion-engine-driven water wheel.

 "...just as there is no smooth gradient to the production of a bacterial flagellum. This conclusion is supported by knockout experiments confirming the functional holism of the flagellum, and also by theoretical considerations of the physical, chemical, and engineering requirements for selectable motility."

But consider; an ox-driven water wheel works; it's just not as fast etc. as a motor-driven one.  But the physical, chemical, and engineering requirements for selectable motility, whatever that means, are surely met by both systems.

He then adds, that however, "it is very interesting to consider what a smooth, gradually sloping fitness function capable of generating a bacterial flagellum would have to look like.  We know it would have to select for intermediate structures and proteins to be used in the future flagellum.  But the intermediate structures do not function..."

 Again, we find an invalid assumption; namely that "intermediate structures do not function."  Nonetheless, Bracht continues:

 "...so the fitness function must somehow make it possible to preserve these useless, functionless proteins until the entire flagellum has been generated in small steps over many generations.  Under such conditions it would be reasonable to expect the flagellum to arise with high probability, but the fitness function required is so obviously contrived as to constitute a remarkable instance of teleology: obviously, nature would have to want to produce the flagellum and to be willing to do a lot of counterproductive work to get that goal accomplished.  Furthermore, the fitness function in this example contains all the details of a bacterial flagellum-nothing is output that wasn't originally present in the fitness function.  This is precisely how Young's coin-tossing machines operate, and this is precisely why they fail as an example of how biological information can be generated by Darwinian processes.  They incorporate a non-Darwinian teleological fitness function that sneaks in the very information they output."

Another invalid assumption!  Upon this, Bracht builds the following:

 "These sorts of biological structures require large amounts of information be generated in a single step.  This is the key problem facing a Darwinian explanation, and is the reason why some doubt the efficacy of natural selection in producing these systems.

"The challenge, and the essence of Darwin's theory, is to show that information can be built up gradually, step-by-step, from initial conditions lacking information.  In Young's example information is conserved; we can easily trace the flow of information from the input parameters to the output sequence of heads.  But this does nothing to address the central claim of the Darwinian mechanism-which is that information can gradually accrue from simple and information-poor beginnings.  If Matt Young wants to demonstrate how information arises in the first place, rather than how it can be transmitted once it has arisen, he needs to do better than talk about knotty pine and corroding coins."

It is indeed the case that the origin of life from non-life and the inception of the first biological systems is a knotty problem indeed, but this is a distinct problem for how the rest of biological complexity came about through time, which is what Darwinian theory addresses.