(You can read my take on these books: Miller's, and Coyne's).
The heart of the issue is this: do you have to twist the science in order to fit both Christianity and evolution into your beliefs? Coyne says yes, Miller says no. One of Miller's offending statements, where he supposedly manipulates science to fit his theology is this:
What bugs [people opposed to evolution] is that evolution carries with it a message they just don’t want to hear. That message is that we not only live in a natural world, but we are part of it, we emerged from it. Or more accurately, we emerged with it.
To them, that means we are just animals. Our lives are an accident, and our existence is without purpose, meaning or value.
My concern for those who hold that view isn’t just that they are wrong on science, wrong about the nature of the evidence, and mistaken on a fundamental point of biology. It’s that they are missing something grand and beautiful and personally enriching.
Evolution isn’t just a take-it-or-leave-it story about where we came from. It’s an epic at the centre of life itself. It tells us we are part of nature in every respect. Far from robbing our lives of meaning, it instils an appreciation for the beautiful, enduring, and ultimately triumphant phenomenon of life.
Seen in this light, the human presence is not a mistake of nature or a random accident, but a direct consequence of the characteristics of the universe. What evolution tells us is that we are part of a grand, dynamic, and ever-changing fabric of life that covers our planet. Even to a person of faith, in fact especially to a person of faith, an understanding of the evolutionary process should only deepen their appreciation of the scope and wisdom of the creator’s work.
To Coyne, this is slipping religion into science:
To say that our lives are anything other than an accident (including, of course, the accidents of meiosis and of which sperm makes it to the egg), buys into the idea — one that Miller has promulgated –that the appearance of humans or something like us was inevitable. Indeed, he explicitly stresses this inevitability when he says our lives are “a direct consequence of the characteristics of the universe.” Well, yes, and so are the lives of squirrels and redwoods. But what Miller really means here –and we can have no doubt about this given the content of his talks and writings –is that the laws of the universe are fine-tuned for the appearance of humans, and that, given the nature of evolution and Earth, the appearance of higher intellectual capabilities (ones that could apprehend and worship their Creator) is inevitable.
What bothers me is that Miller can’t resist slipping in, under the guise of his expertise as a biologist, the idea that it is scientific to assert that the laws of physics are fine-tuned for our appearance, as is the nature of the evolutionary process itself. But those are NOT scientific statements; they are philosophy born of religion. That’s why I don’t think people who represent the public face of evolution should mix their magisteria. It gives the authority of science to statements for which we have either no evidence, or counterevidence.
Coyne's own preconceptions on this issue have blinded him to the fact that there is a large group of non-religious scientists who have come to exactly the same conclusions I have with respect to the ability of evolution to produce intelligent life. Who are these folks? They include everyone who has worked in, supported, or argued for SETI, the search for extraterrestrial intelligence. Most prominent among them would be the late Carl Sagan. Sagan's confidence that intelligent life would be found elsewhere in the universe most certainly did not stem from religious convictions — he was an outspoken atheist — but from an analysis of the vastness of the universe and the inherent capacity of matter to give rise to life.
I am not a theist or deist or believer of any sort - my religious outlook would be hard to differentiate from that of Coyne, PZ Myers, Richard Dawkins, or Richard Feynman. But I'm siding with Miller here: to say that "our lives are a direct consequence of the characteristics of the universe" is not a claim that the universe was purposely fine-tuned for us; it's essentially just a statement of the weak anthropic principle, and Miller has, in multiple places, explicitly denied that he is arguing that the universe was set up explicitly to produce the species Homo sapiens.
In fact, substitute 'solar system' or 'galaxy' or 'life' for 'human presence' in Miller's statement above, and it becomes more obvious how uncontroversial Miller's claim is. 'Accident' is frankly a bad term, playing into the creationist notion that what we observe around us is so improbable, that natural laws couldn't possibly have produced it. Contingent, yes, but accidental no; as Stuart Kauffman says, we're at home in the universe. The development of life from pre-biotic chemical systems, and the evolution of consciousness, is not going to happen anywhere else in the universe exactly as it happened here, but it's extremly probable that life and intelligence have developed in some form elsewhere. If not, origins-of-life researchers like Dave Deamer are pursuing a hopeless research program.
This is one of the most awe-inspiring features of our universe - that it can produce such amazing complex systems. The idea that scientists can understand the origins of life from non-life, or the evolution of complex living systems, in the same way that they understand the evolution of nebulae and solar systems, came to me as an epiphany in grad school, and has driven my research interests ever since. Miller absoutely right to say that "Far from robbing our lives of meaning, it instils an appreciation for the beautiful, enduring, and ultimately triumphant phenomenon of life."
And if theists want to argue that this can be consistent with their theological beliefs, fine: we've now left the realm of science and entered theology and philosophy. Maybe Miller holds some inconsistent beliefs; well, we all do, and that shouldn't disqualify us from being scientists. The bottom line, though, is that Miller has not distorted the science.
There is one more element to this debate: I think Jerry Coyne is insane to fight this battle, one in which he's taken on some of the most effective public defenders of evolution education around. Although scientists are more likely than not to have doubts about God, there are still large numbers of believing scientists, and even larger numbers of students, parents, politicians, voters, and taxpayers who are theists. If evolutionary biology is a direct assault on religion, why should these people support it in our schools and grant-funded labs? Since Coyne is not about to convince most people to give up their religion, the only kind of victory he can achieve here is the pyrrhic sort.
There is more than scientist self-interest at stake here too. Science is one of the outstanding human achievements. Let's not turn curious minds away from it with mistaken claims that the most prominent Christian scientists can only maintain their belief by short-changing or distorting the science. The fact is that there are people who are both outstanding scientists and devout religious believers, and attacking these people really doesn't achieve much.