Considering the critical role of cellular energy production in human health and metabolic operations, why in the world would an intelligent designer have entrusted so much of the production process to a mitochondrion, given the outrageous molecular features this organelle possesses?. Why would a wise designer have imbued mtDNA with some but not all of the genes necessary to carry out its metabolic role (and then put the remaining genes in the mucleus instead)? Why would a wise engineer have put any crucial genes in a caustic cytoplasmic environment where they are exposed routinely to high concentrations of mutagenic oxygen radicals? And why would He have dictated that the mitochondrial genetic code must differ from the nuclear genetic code, thereby precluding cross-translation between two genomes for which effective communication would seem to be highly desirable?
The puzzlement for explanations involving ID goes even further. Why would an intelligent designer have engineered mtDNA structures (such as a closed-circular genome, no introns, no junk DNA, lack of binding histones) and mtDNA operations (such as little or no genetic recombination, the production of a polygenic transcript, a limited ability to mend itself, and no self-sufficiency in transcription or translation) to differ so fundamentally from their counterpart features in the nuclear genome? In a nutshell, the underlying design of the whole mitochondrial operation seems to make no (theo)logical sense. Not only is the overall design of mtDNA suboptimal—it is downright ludicrous. [103-4]
However, as discussed in chapter 1, in this book we are not particularly concerned with genomic features that suggest good workmanship because such features are philosophically consistent with either natural selection or intelligent causation. Our focus instead is on genomic features that defy notions of a supreme intelligence underlying biological design. Genomic flaws should in principle provide a more decisive test of whether unconscious evolutionary processes or cognitive agents have shaped our genes. 
Evolutionists have been making these arguments for centuries but what many observers, including historians and philosophers of science, fail to realize is that these arguments are metaphysical. One reason for this failure is that these evolutionary claims are rather charged and polarizing. People tend to agree or disagree with them, and hence the debate rapidly focuses on whether or not evolutionary claims are true.
While certainly that is an interesting question and worthy of discussion at some point, it misses the more fundamental point which is that evolutionary thinking is metaphysical. It may be true, it may be false, but it is metaphysical.
The claim that evolution is overwhelmingly a fact is underwritten not by the science (on which evolution is problematic), but by the metaphysics. For instance, set the debate aside for a moment and take the evolutionary position. Assume, for a moment, that you believe what evolutionists believe. Pretend that you, rather than the evolutionist, wrote the above passages. Now ask yourself, is evolution a fact?
Of course it is. It must be. Once you understand evolutionary thinking, then you will understand why they say evolution is a fact. Evolutionists claim the high ground of science and accuse others of religious bias. But it is all a hypocritical lie.
And when confronted with this evolutionists equivocate on their claims. They say the “fact” of evolution refers merely to change over time. That equivocation is easily exposed and it reveals how twisted is evolutionary thinking. Oh what a tangled web we weave.