We've seen that Behe's argument turns on two key claims:
(i) Some biochemical systems are irreducibly (very) complex
(ii) Irreducibly (very) complex systems can't plausibly be accounted for in terms of evolution.
Thus, if one rebuts (i.e., shows false or otherwise contrary to reason), or at least undercuts (i.e., undermines the evidence for), (i) or (ii), then one has shown that Behe's argument is a failure. We've seen that Draper has offered apparently decisive criticisms against (i), and thus has already defeated Behe's argument. However, Draper goes beyond this and offers two main criticisms of (ii) as well -- i.e., he argues that evolution can produce a biochemical system even if it's irreducibly complex. In the current installment, we'll focus on Draper's first main criticism of (ii).
II. Behe's Argument Against Indirect Pathways
Recall the two routes or pathways that evolution can take to producing a given biological system -- direct and indirect -- and that an indirect evolutionary pathway is one that creates a system by changing either its function or its mechanism (or both). Further, recall Behe's claim that it's extremely improbable for an irreducibly complex system to be created via an indirect evolutionary pathway. Why are we supposed to think this? Behe's answer consists in an analysis of one possible kind of indirect pathway, which can be stated in terms of a two-stage developmental sequence:
Stage 1: Two or more separate, independent systems arise, whether reducibly complex or irreducibly complex.
Stage 2: Once they are all "up and running", the parts from these different systems begin to interact, thereby becoming parts of a new system performing a new function.
Behe then argues that this indirect pathway to an irreducibly complex system is too improbable to be a plausible explanation. To see why, recall Behe's original definition of irreducible complexity:
(IC1) A system S is irreducibly complex if and only if:
(i) S is composed of several interacting parts
(ii) S's parts are well-matched
(iii) removal of one or more of S's parts would cause S to cease functioning
Now in our previous installments on Draper and Behe, we focused on the way in which Behe exploits clause (iii) of IC1 to argue against the evolution of irreducibly complex systems. But in his argument against indirect routes to irreducibly complex systems, he exploits clause (ii): that the parts are well-matched; that is, the parts are tailored to one another in such a way that the size, shape, etc. of each part is much better-suited to interact with the relevant other parts than if they had different sizes, shapes, etc.
With these ideas before us, we're now in a position to understand Behe's argument for why indirect pathways to irreducibly complex systems are too improbable to be a plausible explanation: if the system in question is irreducibly complex, then by clause (ii) of (IC1), its parts are well-matched. But if so, then the move from stage 1 to stage 2 would require the parts to be well-matched before they could interact in a way for the new, irreducibly complex system to function. But tailoring the parts to make them well-matched takes time, and the new system would be non-functional until then. But if so, then evolution would eliminate the system before that ever happened. Therefore, it's too improbable for an indirect evolutionary pathway to get us from stage 1 to stage 2.
III. Draper's Criticisms
What to make of this argument? Draper makes two points in his reply. First, even if Behe is right, he can't reach this conclusion with the notion of well-matched parts in clause (ii) of IC1. For, at least in principle, a system might perform its function at least poorly without well-matched parts, and so the new system at stage 2 could do so for a time, in which case it would be functional while evolutionary processes finished fine-tuning the parts of the system until they are well-matched. Thus, in order to block this possibility, Behe would need to revise his account of irreducible complexity again, such that an irreducibly complex system's parts aren't just well-matched, but irreducibly well-matched. Since we saw last time that he has aleady revised (what we're calling) IC1 once before to (what we've called) IC2 (to some handle criticisms of his argument in the literature), we'll call the new definition 'IC3':
(IC3) A system S is irreducibly complex if and only if:
(i) S is composed of several interacting parts
(ii') S's parts are well-matched to such a degree that even fairly minor alterations to their shapes, sizes, etc. would cause S to cease functioning
(iii') A subset x of S's parts are such that removal of one or more of x's parts would cause S to cease functioning
This brings us to Draper's second point: even the irreducible well-matchedness of parts in a system that satisfies IC3 isn't sufficient to put indirect routes to irreducibly complex systems beyond reasonable probabilities. For while Draper grants that Behe's own example of an indirect pathway to such a system may well be ruled out if we assume IC3, there are lots of other possible indirect pathways to irreducible complexity that Behe doesn't discuss, and these haven't been shown to be beyond reasonable probability -- even assuming their parts are irreducibly well-matched. Draper sketches the relevant pathway here as follows:
"The sort of route I have in mind occurs when an irreducibly complex and irreducibly specific [his expression for our 'irreducibly well-matched'] system S that serves function F evolves from a precursor S* that shares many of S's parts but serves a different function F*. Notice that parts that S and S* share and that are required for S to perform F need not be required for S* to perform F* even if they contribute to F*, and parts that are irreducibly specific relative to F may only be reducibly specific relative to F*. Thus, both S* and the specificity of its parts may have been gradually produced via a direct evolutionary path. Then one or more additional parts are added to S*, resulting in a change of function from F* to F. And relative to F, the parts and their specificity, which had not been essential to F*, are now essential."
In sum, even if Behe could solve the worries for his claim that at least some biochemical systems are irreducibly complex, his other key claim -- that such systems can't arise via evolution -- is undercut.
But Draper doesn't end his criticisms here. In the next and final installment, we'll see that Draper undercuts Behe's claim that direct evolutionary pathways to irreducibly complex systems are impossible.
 "Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously." Behe, Darwin's Black Box, P. 40.
 Draper, "Irreducible Complexity and Darwinian Gradualism: A Reply to Michael J. Behe", Faith and Philosophy 19:1 (2002), pp. 3-21.