@Chris_Falter, I thought I would check into some of Denton's thinking. I have to say, it doesn't seem like he has much conviction to any such belief in common descent.
Let's look at this chunk of logic and thinking:
"Denton suggested that these data undermined the notion that fish were ancestral to frogs, which were ancestral to reptiles, which were ancestral to birds and mammals. If they were, then wouldn't the difference in cytochrome C structures be increasingly different from carp to frog, to reptile, to mammal? How could the cytochrome c amino acid sequences for such a wide range of species all be "equidistant" from the sequence for bacteria? "
In the very first sentence, you see Denton challenging something as basic as fish came before amphibians, and amphibeans came before reptiles! If Denton thinks God-Guided evolution is the "main-chance", he's got a funny way of making the point!
The paragraphs below is a discussion of why Denton's criticism didn't make much of an impact.
"Molecular biologists quickly pointed out the fallacy in Denton's argument. Just as there is no such thing as a "living fossil", and all modern species are cousins, so too, the amino acid sequences for all living species have been evolving since the time of their divergence from a common ancestor." 
[Footnote 14: Spieth, Philip T. (June 1987). "Review – Evolution: A Theory in Crisis". Zygon. 22 (2): 249–268. doi:10.1111/j.1467-9744.1987.tb00849.x.]
"A modern carp is not an ancestor to a frog; frogs are not ancestors to turtles; turtles are not ancestors to rabbits. Similarly, the variations in eukaryotic cytochrome c structure with respect to bacteria are all due to mutations taking place since divergence from the common ancestor of these different organisms. It thus is not surprising that they show a similar level of divergence and equidistance of this type was even predicted and confirmed by researchers as early as 1963." 
[Footnote 15: A Tale of Two Crocoducks: Creationist Misuses of Molecular Evolution, James R. Hofmann ]
As recently as 2014, Denton has fired off another frontal assault on the fundamental premise of Evolutionary science .... that a lot of little changes can frequently lead to Speciation - - launching his verbage against the darlings of Darwin - - the finches of the Galapagos!:
"From the emerging developmental genetic picture, it is now relatively easy to envisage how gradual adaptive fine-tuning of the expression patterns of a handful of genes could result in the different beak forms of the Galapagos finches we see today."
"The evolution of finch beaks requires no causal agency beyond natural selection. Some finch beaks proved advantageous; others, not. The lesson of the Galapagos, and all such cases of microevolution, is that cumulative selection will work its magic just so long as there is an empirically known or plausible functional continuum, at the morphological or genetic level, leading from an ancestral species or structure to a descendent species or structure."
What is ironic about Denton's opposition is that he seems to genuinely believe that God has created life forms through his direct intervention - - and yet simultaneously rejects the idea that God would use evolution to create new Species!
How does one pursue both lines of reasoning simultaneously? How does God guide evolution if when God spends a million years to create a brand new life form - - he has to do it WITHOUT creating a new species? How is this even logically sensible?
If God guides evolution ... there has to be Speciation!!! Unless you are going to argue that Whales are just a degenerated branch of the same species of Amphibians!
If God's intelligent design is in use to create new forms of life .... unless God is "POOFING" these life forms into existence .... then speciation is STILL required.