Critics argue that Intelligent Design identifies gaps in current evolutionary explanations and then attributes those gaps to design. Because scientific explanations can improve as new evidence is discovered, an argument based only upon what science does not presently know would become weaker whenever a new mechanism or historical pathway is found.
This objection concerns the logic of the design argument itself. A genuine gap in present knowledge is not automatically evidence for design. Scientific history contains many examples in which previously unexplained phenomena later received natural explanations.
The objection is valid against a design argument that consists only of saying, "Evolution has not explained this, therefore it was designed." A stronger design argument would need positive reasons for recognizing purposeful organization and would need to engage seriously with known evolutionary mechanisms.
That is why this investigation has examined mutation, selection, experimental evolution, gene duplication, gene birth, protein evolution, regulatory change, speciation, development, and convergence before considering explanatory limits. Demonstrated evolutionary capabilities should be incorporated rather than ignored.
The remaining issue is whether there are features for which positive indicators of purposeful organization can be identified and whether design provides explanatory value beyond pointing to incomplete evolutionary knowledge.
What positive evidence would distinguish purposeful organization from a temporary gap in evolutionary knowledge, and what observations could count against a proposed design explanation?