Vestigial organs are sometimes used as part of an argument from poor design and as a counter argument to the argument from design. A benevolent god would presumably not add vestigial organs to species. However, evolution allows for organs which have lost their original use, as well as to potentially develop an entirely different adopted function. The debate surrounding vestigial organs is often mired in confusion surrounding definitions:
- "In evolutionary biology and comparative anatomy, "vestigiality" in a species describes organs (vestigial organs), structures (vestigial structures), behaviors, and biochemical pathways that have seemingly lost all or most of an original function present in ancestor species. These structures are typically in a degenerate, atrophied, or rudimentary condition [...]"
- "In a sense, vestigial remains are like footprints leading us back to an earlier time when they were fully developed, a time when the ancestral animal had a significantly different body structure and a totally different way of life from the example alive today."
"An organ, serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose, and remain perfectly efficient for the other. [...] Again, an organ may become rudimentary for its proper purpose, and be used for a distinct one: in certain fishes the swimbladder seems to be rudimentary for its proper function of giving buoyancy, but has become converted into a nascent breathing organ or lung. Many similar instances could be given."
A vestigial organ sometimes misleadingly (or historically) defined as a "functionless organ". While the evidence for vestigial organs is strong, junk DNA arguably provides even stronger examples for features that have lost their original functions.
- Wings of flightless birds 
- Limbs in cetaceans (whales and dolphins) 
- Snakes having legs 
- Eyes in blind cave fish 
- Body hair in humans 
- Wisdom teeth in humans 
- Goose bump muscles in humans 
- Many aspects of our psychology are, in a sense, vestigial
Examples are in fact purposeful
- "As with many other mystery organs relegated to the vestigial evolutionary waste bin—metaphorically if not literally, since fortunately most are not so exposed for easy excision—the appendix eventually began to be rehabilitated as medical science found it impossible to ignore additional evidence of its important roles both before and after birth."
Vestigial organs are not useless organs but organs that have lost their original function.
We live in a fallen world
- "It is often assumed by the anti-God brigade, though unvoiced, that the designer created everything as we see it today. Within the biblical model, degeneration is expected because of the Fall."
The apologist is trying to have it both ways: humans are both well designed for modern existence (according to the argument from design), and for life in Eden rather than modern life (according to this counter argument). Their admission that life is not well suited for its environment undercuts their main argument and is an example of mutually-contradictory apologetics.
Possible argument from ignorance
- "The problem with declaring any organ to be without function is discriminating between truly functionless organs and those that have functions that are simply unknown."
This is certainly a concern. However, vestigial organs are not "functionless organs". Scientists can determine the original function of a biological structure with a high degree of certainty: for example wings are originally for flying or gliding. Although they may have found some utility in flightless birds, that does not make them non-vestigial in those species.