Here’s an example. It has been known since Aristotle that species tend to cluster in a hierarchical pattern and in the eighteenth century Linnaeus saw it as a reflection of the Creator’s divine plan. Obviously this pattern does not force one to embrace evolution. But does it really look like a divine plan? Darwin argued it most certainly did not:
The several subordinate groups in any class cannot be ranked in a single file, but seem clustered round points, and these round other points, and so on in almost endless cycles. If species had been independently created, no explanation would have been possible of this kind of classification.
This argument about divine patterns did not begin with Darwin. It has complex theological roots, and today it continues as one of evolution’s many metaphysical axioms. Fifty years ago evolutionist George Carter explained that “If species are separately created there is no reason why they should be created in large groups of fundamentally similar structure.”
Niles Eldredge agrees that the pattern defies creationism and design:
Could the single artisan, who has no one but himself from whom to steal designs, possibly be the explanation for why the Creator fashioned life in a hierarchical fashion—why, for example, reptiles, amphibians, mammals, and birds all share the same limb structure?
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.” 
Of course this claim about how the species would be designed does not come from science. Nor do the many other metaphysical claims that, over and over, prove evolution.
For instance, another common metaphysical mandate is that god or a designer would never draw up inefficient designs. A favorite example is the recurrent laryngeal nerve which, Coyne explains,
makes no sense under the idea of special creation ... No form of creationism/intelligent design can explain these imperfections …
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 ultimate truths which are far beyond the halls of science.
Is this enough for us to convict evolution? Actually no, metaphysics is no sin. There’s certainly nothing wrong with holding religious beliefs. And is there anything wrong with viewing the world through the spectacles of one’s beliefs?
Indeed, who says there is anything wrong with allowing one’s beliefs to influence science? Well, in fact evolutionists say this, and herein lies the rub. The problem is not that evolution is a metaphysical theory or that evolutionists promote their metaphysical views. The problem is that evolutionists criticize others for precisely what they do. They even deny what they do. As Jerry Coyne explains, our metaphysics are really not metaphysics at all:
the argument from imperfection — i.e., organisms show imperfections of “design” that constitute evidence for evolution — is not a theological argument, but a scientific one. The reason why the recurrent laryngeal nerve, for example, makes a big detour around the aorta before attaching to the larynx is perfectly understandable by evolution (the nerve and artery used to line up, but the artery evolved backwards, constraining the nerve to move with it), but makes no sense under the idea of special creation — unless, that is, you believe that the creator designed things to make them look as if they evolved. No form of creationism/intelligent design can explain these imperfections, but they all, as Dobzhansky said, “make sense in the light of evolution.”
Should we laugh or cry? According to Coyne the design “makes no sense under the idea of special creation" and this "is not a theological argument, but a scientific one.” Coyne’s misrepresentations and sophistry are astonishing. The problem is not that evolutionists are metaphysicians—the problem is that they are in denial, and in the process make a mockery of science. Religion drives science and it matters.