A very helpful article with excellent examples and clear explanations. Thanks!
I would add a fifth example: biologists have developed two tools that predict protein function from genetic sequences: BLAST and SIFTER. BLAST uses similarity heuristics, which could be classified as a design concept (similar design for similar function). SIFTER takes a different approach by inferring a nested hierarchy, then using the hierarchy as a critical factor in predicting function. SIFTER’s approach is thus based on the concept of common descent via a model of nested hierarchy.
To determine whether common descent or common design is a better model, you can see which model does a better job of predicting protein function, with BLAST and SIFTER serving as proxies for common design and common descent, respectively. It turns out that SIFTER (the common descent proxy) provides far more accurate predictions of protein function than BLAST. This comparison between the tools shows that common descent yields far better predictions than common descent by itself.
This comparison is discussed in a lengthy forum thread from 2017 started by our friend @Swamidass .
Best,
Chris Falter