I just came across a good article by Biologos editor Jim Stump, which discusses four biological examples that are explained better by “Common Descent” (evolution) than by “Common Design” (each species created separately):
Common Descent Explanation: The evidence we see—of shared characteristics in plants and animals alive today, and in the fossil record—is best explained by supposing that they descended from common ancestors.
Common Design Explanation: That same evidence can be explained equally well by supposing a Designer created species or kinds separately—that is to say they don’t have common ancestry—but used a common design template for those characteristics that are similar.
The four examples covered in the article are:
- Example 1: Mammalian Skeletons
- Example 2: Amino Acid Specification
- Example 3: Vitamin C Producing Genes
- Example 4: Mutation Signatures
I recommend reading the original Biologos article. Here I will summarize key points from the first and the third examples.
Example 1: Mammalian Skeletons
Most mammals run around on four legs, but there are mammals which swim in the water, fly in the air, and walk on two legs:
If God designs things the way human engineers do, then we might reasonably expect the intended function of the “machine” to drive the design process.
It is curious, then, that the design plan of mammals has been used for so many different functions when there were other design plans available for those functions…It seems that a human designer would have borrowed more directly from the bird body plan in designing bats, and from the fish skeleton in designing whales and dolphins.
…The mammalian skeleton, adapted as it is to these different ways of moving around in the world, is exactly what is predicted by mammals (including us) having ancestors in common. In order for these skeletons to work as evidence for Design, you need to add some plausible reasons why God would create in a way that fits Descent so well. Perhaps one could rustle up some such reasons, but it must be admitted that Descent is a simpler, more straightforward explanation of this evidence.
Example 3: Vitamin C Producing Genes
Most animals are able to synthesize vitamin C (ascorbic acid) in their bodies. Vitamin C synthesis is a multistep process, which depends on enzymes produced by certain genes.
Among mammals, however, there are a few groups that cannot produce vitamin C, so they need to eat it in their food. Humans are one of these species; we get scurvy if we do not consume enough vitamin C in our diets. It has been found that all primates which cannot synthesize vitamin C have mutations in a particular gene (the “GULO” gene), which render it ineffective.
The Biologos article comments:
The best explanation of this observable evidence is that the mutation occurred long ago in the common ancestors of humans, apes, and monkeys. That’s why we find the same broken gene in all these species today. It would be too remarkable to suppose that the same gene in all of those species independently mutated the same way.
Couldn’t Design work just as well here? We might hypothesize that God has reasons for creating some species without the ability to synthesize vitamin C, and that “mutated” gene is built into the common design plan.
Just like the first two examples I’ve offered, we can admit that there might be reasons why God would do it this way. But we must also admit that it is a more complex and ad hoc explanation than what seems pretty straightforward according to Descent. Furthermore, in this example there is an even bigger problem for Design.
Another piece of data has to be reckoned with: guinea pigs and fruit bats also can’t make their own vitamin C. This generates very specific predictions from the two explanatory models. Let’s start with Design.
In order to explain why humans, chimps, other apes, and monkeys can’t synthesize vitamin C, and why they all have the same broken gene, Design proposes that God must have had some reason why these animals shouldn’t be able to make their own vitamin C, and used the common design plan that included the defective gene. Now we have two more animals that can’t make vitamin C, and so we’d expect there to be a reason why God wanted it that way, and for this same design plan to be used for them too. [I.e., we’d expect the gene to be broken in the same way in these other animals]. But this prediction turns out to be false. The inability of guinea pigs to produce vitamin C is the result of that gene being broken in a different way  than it is broken in humans, other apes, and monkeys. And the gene in fruit bats is broken in a yet different way than either guinea pigs or the human group.
Of course, that is exactly what Descent predicts we’d find. Look at the graphic of the Mammal Family Tree (above). If we had discovered that the gene for all these animals was broken in the same way, we would have to suppose there was a mutation event back in the common ancestors of all of them. But then all their descendants would be expected to have that defective gene. And that is not what we find. Other rodents, lemurs, hoofed animals, and other kinds of bats can all make their own vitamin C. So instead, it is more reasonable to suppose that there were different mutation events for guinea pigs and for fruit bats. Those mutations should look different according to Descent because there are many ways to break a gene, and it would be unlikely for it to break in exactly the same way twice. And that is exactly what we find.
Why Does This Matter?
The Biologos article concludes by noting that these biological findings do not present difficulties for Judeo-Christian faith:
In each of these examples, Descent provides a simpler and more straightforward explanation for what we observe. There is no need to try to guess why God did things contrary to what we would expect. But that doesn’t mean that God had nothing to do with this process.
At BioLogos, we’re happy to acknowledge God as the designer, creator, and sustainer of all that exists. We do not believe God to be an absentee or deistic God who merely created matter and let it go on its own. But we don’t think God’s ongoing involvement in the created order is best affirmed by rejecting the scientific consensus of well-confirmed explanations like Descent. Instead we see God’s amazing provision for his creation in the scientific details we have been privileged to uncover.
I would add that this position entails not reading the Genesis creation story simplistically. I do not claim to have the only or the best answer here, but some of my thoughts on biblical hermeneutics are here and here.
 In this linked video by Stephen Schaffner on human genetics, the discussion on vitamin C begins at about the 19 minute mark.