The theory of evolution is that microscopic organisms evolved into whales in a period of about a hundred million decades. I use decades, rather than years or seconds, because it takes 2 decades for a fertilized human egg to produce all of the cells in the human body.
Whether evolution is a fact or a theory, natural selection acting upon innovations is an attempt to understand what caused evolution. The old paradigm for innovations is random mutations, but the new paradigm is natural genetic engineering, at least according to James Shapiro of the University of Chicago.
Whatever the paradigm, evolutionary biologists don’t understand how mammals evolved in such a short period of time. This is expressed by saying natural selection explains the adaptation of species to the environment (microevolution), but not common descent (macroevolution).
Consider hemoglobin, the protein that carries oxygen to cells. The primary structure of hemoglobin is a chain of 600 amino acids. There are twenty different amino acids and every amino acid must be in exactly the right position on the chain. Sickle-cell anemia is caused by one misplaced amino acid. Hemoglobin is like an English sonnet with the 26 letters taking the place of the 20 amino acids. Since it is virtually impossible for a computer to generate a sonnet by randomly selecting letters, natural selection cannot explain even the primary structure of a protein.
The only theory that even attempts to explain evolution is the theory of intelligent design (ID), and Meyer is an advocate of ID. However, ID is irrational because there is no evidence that an intelligent designer exists.
Meyer thinks there is evidence for ID because he doesn’t consider the possibility that the universe is not intelligible. The existence of proteins is evidence that the universe is unintelligible. It is not evidence for an intelligent designer. The theory that an intelligent designer exists is an exercise in circular reasoning. As Richard Dawkins put it, “Who designed the designer?”
Meyer also uses the straw man argument by implying that evolutionary biologists who are against ID think natural selection explains evolution. This scam succeeds because atheists go along with the scam. Atheists don’t want to admit that ID is a better theory than natural selection in some sense. Both atheists and advocates of ID are more interested in promoting their religious enthusiasms than in promoting an understanding of evolutionary biology.
Meyer tries to explain why ID qualifies as science notwithstanding the objections of those who advocate “methodological naturalism” and “materialism.” This is the case of the blind leading the blind. Human beings ask scientific questions (Why is the sky blue?) and metaphysical questions (What is knowing the sky is blue?). The answer to the metaphysical question is that it is a mystery. This means humans are embodied spirits and finite beings. Since finite beings need a cause, an infinite being exists. We call the infinite being God, Brahmin, Nirvana, Heaven, Tao, and Shangdi.