The book's underlying argument: because science prescribes to methodological naturalism, Darwin, by following this methodology, proposed the theory of natural selection thereby leaving God out. "That evolution must be godless to be scientific is the Darwin Myth, so profoundly misleading that it must be called a great lie,..." (pxi) According to the author then, this myth has supposedly distorted our understanding of the scientific evidence and the debates surrounding evolution (but not any scientific debates). So the author's core complaint here is with methodological naturalism generally, and Darwin's adherence to it in formulating the theory of natural selection.
Simply stated, methodological naturalism mandates that hypotheses or the causes behind phenomena are to be explained using only natural processes. Supernatural or theistic explanations are not admitted at the outset. It's not that scientists don't believe there is a God; it's just that introducing 'Him' into the explanatory process is irrelevant. The reason for this is that methodological naturalism has been enormously successful in providing explanations, in furthering research and in providing practical engineering applications for example. Science, per definitionem *is* methodological naturalism.
Even though science arose out of disciplines more mystical in nature (as in alchemy becoming chemistry for instance), the superstitious side sent countless individuals down nonproductive alleys and dead ends. Supernatural explanations (if there is such a thing) are unproductive. They really don't explain anything. In spite of there always being some things currently deemed supernatural or inexplicable, they may or may not be explained in the future as some unusual natural phenomena. But it doesn't follow that because science doesn't currently have an answer, that the explanation *must* resort to a supernatural one.
Additionally, the idea that a supreme being created everything or intervened is not the only supernatural hypothesis one could propose. The list could be endless: from lesser gods to evil spirits, demons, Satan, goblins, mind control, psychic energy, aliens? etc. How would one eliminate the panoply of possibilities? How would one, by empirical means determine whether a particular event is the work of God or Satan for example?
The author complains about the Origin's 4th edition containing a reference to the creator as being merely a sop--a concession to appease the religious--but it actually shows that it makes no difference to Darwin's basic argument whether a creator is added in or not. Darwin is just saying that once life got started, it diversified via the process of natural selection without *any* interference from God. He doesn't really discuss the origin of life from non-life (abiogenesis). This point is continually lost on creationists discussing origins or Darwin or evolution.
A reasonable job is done in providing a biographical portrait of Darwin and the genesis of his theory. We are told that we're going to get a more honest rendering; one that is without the usual heroic Whig history that usually issues from other Darwin biographers (who are Darwinists no doubt). He gives us the 'straight goods' on some items in Darwin's autobiography. One has to wonder how these biographers get it so wrong whereas this Discovery Institute senior is giving us a truer, nonpartisan? account. But Whig science history is appropriate here as Steven Weinberg comments; "What Herbert Butterfield called the Whig interpretation of history is legitimate in the history of science in a way that it is not in the history of politics or culture, because science is cumulative, and permits definite judgments of success or failure." ([...])
So one really can say whether a scientist in the past got it right or wrong. Darwin got it right.
The author examples Mivart's (a contemporary of Darwin) problems he had with Darwin's theory using the flounder's eyes example where, after being born, one eye migrates to the other side of this fish. Mivart can't see how this could possibly happen by natural selection. There's a great answer now and the author is just pointing out the old God-of-the-gaps argument here: we can't explain it so God must of done it. But note that this hasn't explained it either. Why wouldn't God just 'make' a flounder with eyes already on one side so it doesn't have to migrate to one side after it was born? Anyway, Google: Odd Fish Find Contradicts Intelligent-Design Argument.
Trying to say that others previously came up with the idea of evolution and Darwin contributed nothing significant seems disparaging to his contribution and his theory. Lucretius (99-55 BC) didn't believe in new species arising from older ones. He denied that land animals evolved from aquatic ones. Species were born from the earth period. Darwin's grandfather Erasmus (who wrote Zoonomia), had no self-governing systems of how species change such as reproduction, selection, variation and inheritance. Lamarck was wrong. With Vestiges of Creation by Robert Chambers, life spontaneously generated and it was progressive in nature with (Caucasian) Man at the top. Chambers had no transitions; species just suddenly appeared in leaps. There was no discussion of adaptation and variation. If Darwin's theory was like previous ones, why did it hit like such a bombshell then? It's not simply about sales-pitching your idea or having influential friends.
Near the book's end, the tired rhetorical Hitler card is played and 'Darwinism' is indicted for the Nazi atrocities; but this is entirely irrelevant to the veracity of Darwin's theory, his place in science history and the theory's importance within evolutionary biology today. The author's implicit religious undertow here is that we need an absolute moral compass (based on the Bible and Christianity I would guess) to guide our lives. Darwinism--that godless form of natural selection--not only fails to provide one, it supposedly has undermined previous (religious) ones. It also can't explain the origin of our exalted traits such as reasoning, aesthetics or morality. So we supposedly need a more-inclusive theory that does include these: supernatural selection?
Darwin, and all of science for that matter, didn't take God out; just the miracle part was removed. It's not godless natural selection; it's miracle-free natural selection.