“A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”—Max Planck
Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.
Likewise Jerry Coyne explains that the appearance of species through time is “far from random” and “no theory of special creation, or any theory other than evolution, can explain these patterns.”  And why are species so similar? “There is no reason,” explains Coyne, “why a celestial designer, fashioning organisms from scratch like an architect designs buildings, should make new species by remodeling the features of existing ones.” 
No reason? How does Coyne know that?
Another favorite source of proof for evolution is embryology. Here are representative quotes from leading evolutionists:
How does God’s plan for humans and sharks require them to have almost identical embryos? [Douglas Futuyma, Science on Trial: The Case for Evolution, p. 48]
The passage through a fishlike stage by the embryos of the higher vertebrates is not explained by creation, but is readily accounted for as an evolutionary relic. [Tim Berra, Evolution and the Myth of Creationism, p. 22]
Now, we’re not absolutely sure why some species retain much of their evolutionary history during development. The “adding new stuff onto old” principle is just a hypothesis—and explanation for the facts of embryology. It’s hard to prove that it was easier for a developmental program to evolve one way rather than another. But the facts of embryology remain, and make sense only in light of evolution. [Jerry Coyne, Why Evolution is True, p. 78-9]
Of course these claims about creationism and precisely what God would and would not do, are not from science. Nor are the many other metaphysical claims that, over and over, prove evolution.
In fact evolution is drenched in metaphysics. From its early formulations in the Enlightenment years, to Darwin, to today’s refinements, evolution relies on non scientific assumptions. The “fact” of evolution has never been demonstrated without appeal to non scientific truths.
This reasoning is perfectly valid but it is metaphysical—it is based on our definition of a “sensible God.” So while the empirical science reveals the details of why evolution is unlikely, the religious sentiment mandates that evolution is, somehow, true because creationism must be false.
This reliance on the refutation of creationism means that evolution is a religious theory. But some evolutionists deny this. Yes we say creationism has failed, but that doesn’t make evolution religious, explain these evolutionists. One can test the claims of a theory without agreeing or believing in the premises and beliefs of that theory.
The problem is they are not merely testing the claims of creationism. That is a canard that makes no sense. For centuries evolutionists have fervently expounded that God would not have created such a world as this one. This is no academic, dispassionate analysis. In fact most of the evolutionists claims about creationism would not be recognized by most creationists or design advocates.
Evolutionists are not testing the claims of creationism, they are proclaiming their religious beliefs about God and creation. Beliefs that they have proclaimed for centuries.
Imagine if evolutionists were indeed merely testing some claims they had found in their favorite creationist journal. If that were actually the case, then the most evolutionists could claim is that they have falsified a particular theory of creationism. They would not be able to conclude that evolution is the only remaining alternative. There are many, many potential theories of creationism. They would have refuted only one of them and this would tell us very little about evolution. There would be one less competitor, but the monumental scientific problems with evolution would remain. And so would all but one of the competing theories.
The giveaway is in the takeaway. You can tell how serious evolutionists are about their religious premises by their conclusion that evolution must be true. Or in other words, evolutionists can only conclude that evolution is a fact if they are not merely testing a particular form of creationism, but rather are testing universal claims about creationism.
Their conclusion that evolution is a fact means they believe their claims about creationism are universal. For example, Coyne really believes that God would never have created species with the similarities that we find or the embryonic stages we observe.
As Coyne says, no theory other than evolution can explain these patterns. How can Coyne have knowledge about all possible explanations? The answer, of course, is that he cannot have such knowledge. At least not from science. That kind of knowledge only comes from religion.
Religion drives science, and it matters.