Testing ATP Synthase for IC Status

One of the most frequent criticisms of the Intelligent Design (ID) movement is the lack of testable hypotheses offered by proponents, and/or the inability of ID to even form testable hypotheses.While I doubt that no testable hypotheses have been offered, it's my intention to offer a specific testable hypothesis based on an ID assumptions. Furthermore, the test will generate positive quantifiable results. Use of the word 'positive' in this context does not indicate results that support the testers ideas, but in fact, results that doesn't rely on something not happening... pardon the intentional double negative.Being that this is a discussion forum, and a somewhat informal environment, I will forgo attaching formal references but will be more than willing to discuss the basis for my assumptions on an as need to basis.The hypothesis will be based on the concept of Irreducible complexity as described by Behe: A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. The critical thing here is removal of the components... Behe says nothing about altering components.The allegedly IC system we are going to be investigating will be the rotary biological motor ATP SynthaseThere are many variations on the ATP Synthase theme in nature, the simplest enzymes are those present in bacteria and chloroplasts. In general, the minimal complex is thought to consist of 6 unit subunits, alpha, beta, gamma, a, b, and c, with a stoichiometric ratio of 3:3:1:1:2:10-14. While all of these units appear to be essential for function, we will consider the alpha:beta:gamma:c complex to comprise the enzymes irreducible core. The justification for this is as follows: The catalytic site of this enzyme is located at the interface between the alpha and beta subunits. This is where ATP is formed from ADP and inorganic phosphate. The alpha and beta subunits are where the catalytic activity takes place, and thus cannot be removed.The c subunits, which actually form a ring within the membrane, mediate proton flux through the membrane. This is the source of energy that the cell uses to synthesize ATP... the energy of an electrochemical gradient. If there is not proton flux through the membrane, then neither the c subunit ring nor the gamma subunit rotate, hence the c subunits are part of the enzymes IC.Finally, as proton flux is mediated via the c subunit ring, causing rotation of the c subunits, and the asymmetrical gamma subunit within the alpha-beta hexamers central cavity, the conformation (shape) of the alpha and beta subunits change. This change in shape facilitates the synthesis of ATP and ADP. IOW, the gamma subunit, via rotation induces something called the 'binding change mechanism,' and is in part responsible for catalysis. Thus the gamma subunit is part of the ICore.The a and b subunits are thought to stabilize the 'stator' portion of the enzyme relative to the 'rotor' portion. While they are likely important for catalysis, they will not be considered here for theoretical and experimental simplicity.The hypothesis is that the ATP synthase, at the level of the above described ICore, is IC.The test
Now the question here is what are we interested in. We are interested in exploring the tenets of the IC hypothesis. An example would be how well matched must these components really be to yield a functioning enzyme? How well matched are they now? What degree of genetic change can be tolerated before loss of function? We can explore the degree of 'inherent compatibility' via experiments that correlate enzyme functionality with genetic homology. We can further correlate these changes with 'number of generations'. Finally we correlate change in enzyme functionality vs. number of generations.There will be two varieties of mutation that will be explored, those that affect the enzymes active site, and those that affect protein-protein interactions. Active site mutations will directly affect catalysis, while mutations affecting protein-protein interactions will affect the ability of the enzyme to assemble. In this example, the term active site also refers to the enzymes 'substrate binding site,' and associated residues.Predictions
Based on the idea of IC, it is postulated that the enzyme will be able to tolerate only the most highly conservative mutations... an aspartate to a glutamate, an asparagine to a lysine, etc. in the active site residues. Residues that will be critical are not only those the affect catalytic activity directly, but those that the affect substrate binding.
Furthermore, it is predicted that the enzyme will be able to tolerate less homology at the amino acid level in the protein-protein binding regions, relative to the active site, but the tolerated level of aa homology will be roughly equivalent to the known homology that exists between subunits. For example if the homology of the gamma subunits between model species is 80%, then no more than 20% of relevant amino acids can be altered before the ICore breaks down.So the relationship between genetic homology and enzyme functionality will not be entirely linear. Rather the enzyme will cease to function at approximately the above described level of genetic homology.When these minimum relationships are determined, it will be interesting to construct a 'minimal homology' enzyme, and apply selective pressure, ultimately comparing change in enzyme functionality vs. number of generations. IC predicts that this relationship will be non-linear. That is enzyme functionality will not increase in a linear fashion over time.Model Organisms
There are several model organisms we can consider in this scenario, and in fact a variety should be used. The first bug coming to mind is E. Coli. For one thing, at log phase, assuming dichotomous replication, it can reproduce itself once every 20 minutes. In short thousands and thousands of generations can be investigated in a relatively brief period of time... certainly the length of a Ph.D., or long post-doc.Furthermore, there are a wide variety of media available for E. Coli. Different minimal and rich media combinations could be utilized to apply different selective pressure, and the effects could be explored. You could use a 3D type analysis to correlate media glucose concentration, enzyme functionality, and number of generations.The other organism I would use is chlamydomonas... for several reasons. Firstly, it's a eukaryote, and the comparison would be nice. Secondly it's got a single chloroplast that can be easily genetically manipulated. The chloroplast is nice for a couple of other reasons. For example, you could alter the chloroplast ATP synthase, leaving the mitochondrial enzyme in tact. The organism can then be grown on acetate, and supplied varying levels of light as selective pressure. In addition, the amount of light could be kept constant, and the amount of acetate varied. The same type of graphical analysis could be performed here as in the above described examples.A further organism I would consider using is Pseudomonas. This bug seems to have a penchant for adaptation, and some believe actually possesses an extrachromosomal apparatus specifically for the purpose of adaptation. This extrachromosomal DNA could be exploited. Perhaps a variety of selective pressure can induce some sort of positive change in the enzyme in this particular organism. The nice thing about this bug would be the fact that you would be removing the 'random' aspect of mutation. Predictions with this bug could vary among ID proponents, some might see the increased rate of specific directed mutation as a positive thing, while others might think it would have either no effect, or a negative effect overall.In addition to the above selective pressures, a variety of mutagenic chemicals or 'activities' could be applied to each model organism also... ID based hypotheses would predict that the slope of the graph comparing generations, with cellular growth or enzyme functionality would be negative. The longer a critter is exposed to a mutagen, the less fit it becomes both systemically, and at the level of the individual IC system.So... keep in mind this is just a rough sketch of something I've been considering in my head. It's entirely possible that even ID proponents will not agree entirely with my predictions, or the relevance of my particular methods. But nonetheless, here is a testable hypothesis that makes predictions from an ID perspective that will generate positive quantifiable results that can be further examined via a variety of different analyses and correlations.

The critical thing here is removal of the components... Behe says nothing about altering components.

Based on the idea of IC, it is postulated that the enzyme will be able to tolerate only the most highly conservative mutations... an aspartate to a glutamate, an asparagine to a lysine, etc. in the active site residues. Residues that will be critical are not only those the affect catalytic activity directly, but those that the affect substrate binding.

Furthermore, it is predicted that the enzyme will be able to tolerate less homology at the amino acid level in the protein-protein binding regions, relative to the active site, but the tolerated level of aa homology will be roughly equivalent to the known homology that exists between subunits. For example if the homology of the gamma subunits between model species is 80%, then no more than 20% of relevant amino acids can be altered before the ICore breaks down.