Explain the Differences, Not Just The Similarities

Continuing the discussion from BioLogos: Teaching Evolution to Students of Faith:

A common misconception is that evolution is inferred from similarities between organisms, not the differences. Turns out that it is the pattern of similarities and differences that is important. As I explain here…

For example, consider the critique of genome similarity as evidence for common ancestry of humans and the great apes (pp. 479–82, 492–93). Human and chimpanzee genomes are very similar, about 98% similar by some measures. The author does not explain, however, there are ten times less differences between humans and chimpanzee genomes than there are between mice and rat genomes (e.g., see The Chimpanzee Sequencing and Analysis Consortium, “Initial Sequence of the Chimpanzee Genome and Comparison with the Human Genome,” Nature 437 [2005]: 69). Even with different measures, mice and rats are much more different than chimpanzees and humans. Why? Humans and chimpanzees mutate slower and diverged more recently. Likewise, human and chimpanzee Y-chromosomes are more different than the rest of the genome. Why? For the same reason; Y-chromosomes mutate more quickly than the rest of the genome. Remarkably, the increased divergence of Y-chromosomes is presented as evidence against common descent, rather than what it is: clear and quantitative evidence for common descent. It is not just that humans are similar to chimpanzees, the pattern of similarity and differences is readily explained by the empirically verifiable mathematics of evolutionary science. This does not at all demonstrate God never intervened in our origins, but most scientists find this convincing evidence for common descent. A scientifically viable alternative to common descent must offer a better explanation with similar mathematical rigor. However, no such explanation is offered here.
http://themelios.thegospelcoalition.org/review/theistic-evolution-a-scientific-philosophical-and-theological-critique-2

Notice how the increased difference between Y-Chromosomes between Humans and Chimps is evidence for Common Descent? Turns out that evolutionary theory predicts the pattern of similarities and differences. So this objection does not make much sense.

Though, in agreement with @colewd. I’m not sure that the Theobald paper is strong evidence for common descent. Though it does not merely depend on similarities…

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