micro biology is just macro biology zoomed in.

In other words, humans behaviour is that of a virus...zoom in on Phoenix, AZ from space (google earth) and you'll see the random paths and arteries of our existence in the form of roads and bldgs.

The fact that we still sit in traffic hours a day still baffles me.

A post from RF is not showing.  I was gonna quote it, but the graphics most likely wouldn't quote...

Below was my response but I paused prior to going through the math.  You seem to be under-whelmed by it and also have no other pathways to offer, so I will add to it below.




Right, sorry for neglecting this.  You asked to look at the origin of flagellum as the second example.  Flagellum is a cellular propulsion system that makes use of a rotary turbine pump connected to a drive shaft complete with thrust washers, bearings, and seals.  The shaft is connected to a universal joint and a whiplike propeller.

Here again is a good site with detailed models, movies and animations. 

www.npn.jst.go.jp

Despite numerous claims to the contrary it is not known how flagellum could have evolved by any of the known, observed and cataloged evolutionary processes.  If evolution does ever explain the origin of flagellum it will only be through addition of processes that are not currently understood and validated.

The components making up the flagellum contain multiple parts and many of these parts in turn contain multiple protein subcomponents fitted together by binding sites.  Here is a diagram of the high level parts.



The entire structure is built bottom up by a series of precisely timed developmental control, inventory identification, differentiation and management, component transport, positioning jigs, and measuring devices so that in total more than 120 different proteins are involved.

Each of these proteins have very specific structures, shapes, and chemical affinities exposed in order to identify the components it interacts with and reject those that it should not.

Given the number and size of each protein and the number of amino acids involved and available to construct each together with detailed studies of the number of 3-D shapes and chemical binding sites available one can estimate the total number of permutations and therefore the pool of possible components that could be generated.  Instead let's simplify this and presume that all these components are present at one time or another and available in the group of bacteria in time past to enable these components to come together.  Despite the fact that well over 75% of these proteins have no known source, let's stipulate they do.

To further simplify the analysis let's focus on the motor, the stator, the shaft and the propeller.  These four components are required of all rotary motion devices in order to serve the primary function of locomotion.  If any primary component of any of these subsystems is missing, malformed or misplaced the primary function cannot work.  The number of proteins involved in assembly and use of these components is about 70 and the number directly involve in the components is about 34.  These 34 components must be constructed, molded into the correct shape, delivered and placed in the right location at the right time in order to for the the rotary drive system to function.   Furthermore all of the 500 or so other protein components present in the bacteria must be excluded from the system to prevent malfunction.

In order to understand how this might have been constructed by materialistic mechanisms (or not) we need to identify all the pathways to this device that we can.   One that comes immediately to mind is that it was derived by an all in one combination of these parts in a single evolutionary step.  A second option is that motor and stator was a preexisting subcomponent (of 15 proteins) that simultaneously modified to allow attachment of the shaft assembly.  In this way the motor assembly would previously be assembled as a combinatorial object in one step. 

I will pause.  Perhaps you can identify other pathways?

Continuing:

As combinatorial objects, one must choose, position and assemble them all at once.  Each of these is a distinct intermediate step in the process and any of the other steps could interfere without some constraint that would preserve order and prevent alternative configurations or placements or assemblies.

Beginning with selection, the 34 components must be selected from the 500 components contained by a typical bacteria (actually 4300 but again I will simplify).  Let's also assume that for each of these 34 proteins there are 2 suitable alternatives  The odds that these 34 correct components are selected and all others rejected are then (2/500)^34 * 34! since the order is not important  or 8.73*10^-44.  However examination of the flagellum structure has over 20,000 proteins in the filament, and 26 in each of the three rings, 6 in the proximal rod, 120 in the universal joint etc.  Let's use 10 subunits for each of the 34 pieces.  Redoing the math gives us (2/500)^340 * 340! or 2.55*10^-101.  Now we must consider the configuration problem (position and assemble) and then combine the two for a final probability score by this hypothesis.  The math required for this step is quite complex since we are determining the fraction that would result in actual function divided by all the different ways these components could have been assembled after taking consideration of the fact that some function must be preserved.  Dembski performed this math by using perturbation tolerance using Sterling's formula.  After simplifying it for the very small numbers we are dealing he gets p(pertub)~~K^(q-r)N q is the tolerance factor and r is the identity factor.  With N the total number of elements in the assembly (>20,000), one gets a number about 10^-3000 for flagellum.  With numbers this small we need not consider the number of probabilistic resources or specification resources since even the largest combination of the two of them can't exceed 10^150 the universal probability bound.  From these numbers (10^-101 and 10^-3000) as compared to the limit of resources and specification of 10^150, chance is ruled out.  Remember, I did not even consider origination of these elements.

Given in particular the large number of alternative configurations for the 20,000 plus sub-components in flagellum it should be easier to understand why biological self-assembly systems make use of the control, management, transport and configuration proteins to ensure that these components are built according to the intended function.

Now at this point one could object that my hypothesis is limiting, and so again I will ask anyone with an interest to propose an alternative pathway.

Right.  In building out flagellum I used an average of 10 subunits per protein (the filament is 20,000+ while a few parts have five. Clearly 10 is conservative) a correct approach would be to take each one separate but that would have complicated the math and resulted in a number that makes the odds much worse.  In the case of sickle hemoglobin the hypothesis is completely distinct.  It involves the single substitution of one base pair for another.  The subunits don't figure into the formula.



Right, I did not calculate the number of opportunities for flagellum to arise.  I did not because the complexity results were so low that we could have taken every atom in the universe to be the count for bacteria and the vibration frequency of atoms as the replication rate and the entire 13 billion years that this universe is said to be old and use that for the number of opportunities (10^150) and still not even make a dent in the probability numbers from the complexity step.


I agree there has been a large number of bacteria produced on this earth  but compared to 10^-3000 it is insignificant.  I don't think we need to make an adjustment for sickle trait.

I agree that with the flagellum numbers, mine were guesses and they can be improved.  I don't think it will change the conclusion though. 

I understand your point and agree that hemoglobin is a five part structure. 

The reason that the two calculations are different is because of the chance hypotheses I chose.  The HbS hypothesis deals with origination of the mutation which involves substitution of base pairs.  Origination of HbS began with the stipulation that Hb and the entire hemoglobin existed previously so we don't consider localization and assembly.

In the Flagellum example I stipulated origination and therefore skipped past this part to focus instead on localization, placement and configuration of the complete proteins I stipulated.  This portion of the problem requires consideration of the correct number of subunits.  If I were to include the origination problem in flagellum then the odds get far far worse for chance occurrence. 

While HbS from Hb is entirely consistent with evolutionary processes and does not calculate out as a Specified Complex event, in order for material processes to explain flagellum, we need an additional suite of evolutionary processes.  Flagellum does calculate out as being SC.

In short, you use different assumptions and methodology for both. This is so obviously wrong.

Is there a way to use the exactly the same approach to calculate probability for both cases? For example, evolutionary approach is that components in both cases did exist previously and are changing with the same mechanism (mutation, selection).