The argument from the link (http://www.answersingenesis.org/get-answers/features/vestigial-organs) centers around a logic fallacy termed 'begging the question.' The author claims that vestigial structures can't be explained using evolution since: 1) these structures have all been found to have function, and 2) that one must assume evolution to even explain a structure as vestigial.
Invoking a logical fallacy to argue against evolution is ironic as many creationist arguments against scientific theory commit the very same fallacy by begging the question.
- E.g., a common creationist argument proceeds as follows: DNA is a code. Codes can only be designed by conscious thought. DNA must have been made by an intelligent mind.
Begging the question describes an assertion that is supported by evidence reliant upon the assertion being true.
- E.g., the explanation is impossible because there is no chance it would ever occur.
It's easy to identify the circular logic in this example, the premise that 'the explanation is impossible' is supported with evidence that requires the premise to be true. In the previous example concerning DNA, the premise that 'DNA is a code' that 'must have been made by an intelligent mind' is supported because 'codes can only be designed by conscious thought.' This evidence actually assumes conscious design is necessary for the development of a code.
No one is claiming that evolution is true because vestigial structures exist. Evolution by descent with modification is a hypothesis responsible for generating many different predictions. One prediction is the presence of vestigial characters. These are structures inherited from a common ancestor which may no longer be useful for descendants living in a new environment. Lacking any useful function these characters may be lost.
A common system matching this prediction is found among cave organisms. Many different cavefish species have close relatives with sight, however, the cave populations show a common loss of eyesight despite detectable evidence of past eye structure in these organisms. Almost as if the cave species once had eyesight but over many generations slowly lost the ability to see simply because individuals that could see were no more fit than blind individuals. Eyes are demanding structures to develop and could pose a further disadvantage through infection.
These observations and studies into cave species were performed because of the predictions generated from the hypothesis of evolution. The studies provide data which matches the predictions of lost characters in species inhabiting new environments. These studies are used as one means of supporting the evolutionary hypothesis.
The evolutionary explanation of vestigial structures as remnants of once useful features from an ancient ancestor does require an assumption that evolution is true, but as support for the evolutionary hypothesis it matches the prediction very well.
Good hypotheses have explanatory power. Hypotheses must be testable and they should explain how nature works. Evolution fits the bill, it has been tested for over a 150 years and as the popular quote by Theodosius Dobzhansky states, "Nothing in biology makes sense except in the light of evolution."