Important objections deserve to be examined rather than avoided. The questions below identify challenges raised about the evidence and the design inference. Select one to examine the objection, why it matters, the response offered, the question that remains, and the research sources used.
Biologists frequently describe cellular structures as motors, machines, pumps, transport systems, and information-processing systems. But critics of design can reasonably point out that this language describes how these systems function. It does not establish how they originated.
A molecular motor is not literally a miniature human-built electric motor. Mechanical language can be scientifically useful without implying an engineer.
A complex molecular system does not necessarily have to originate with every modern component already in place. Evolution can recruit proteins and structures that originally performed other functions and incorporate them into new systems.
Gene duplication, changes in regulation, modification of existing proteins, and co-option can provide material from which new functional arrangements develop.
A system may cease performing its present function when one of its modern components is removed, yet that does not prove its ancestors could not have performed different functions with fewer parts.
Evolution does not have to construct the present system by adding components one at a time while preserving exactly the same function at every stage.
The bacterial flagellum has often been presented as a major example of irreducible complexity. However, comparative genomics has identified relationships among flagellar proteins, evidence of gene duplication, and connections with other bacterial molecular systems.
Researchers have proposed stepwise histories in which an ancestral core was modified, duplicated, and expanded over evolutionary time.
Proteins in molecular machines often have homologues in other systems. Shared sequences, structures, and functions provide evidence that biological components have evolutionary histories rather than appearing independently in their present forms.
Our knowledge of molecular evolution is incomplete. Critics therefore warn that unexplained steps in the history of a molecular machine should not be treated as evidence of design. Future discoveries may reveal natural pathways that are presently unknown.