But it is no good simply inventing assumptions that help one defend one's pet theory. Rather, what is needed is independent evidence concerning what God (or some other intelligent designer) would have wanted to achieve if he had built the panda ... Gould assumes that if an intelligent designer had made the panda he would have chosen not to give the panda the spur of bone we call a "thumb" and instead would have given the panda some more efficient device. With this unfavorable assumption, the intelligent-design hypothesis has a likelihood of zero, so the hypothesis of chance and the hypothesis of evolution by natural selection both have higher likelihoods. [128, 143]
Gould, of course, did not "invent" assumptions about divine intent as Sober accuses. Such theological assumptions have been popular for centuries, and are crucial in the formulation and justification of evolution by Darwin and evolutionists since. But Sober is correct that it is a powerful religious assumption, rebuking design and therefore pointing to a naturalistic narrative, of one sort or another.
Sober suggests that such assumptions should not be used, but in his new paper approves of precisely this sort of argumentation. Sober explains how common ancestry is indicated, not because it is likely, but because separate ancestry is unlikely. How is this done? By appealing to those "useless and deleterious" designs in nature, such as our tailbone and those invisible gill slits in the human fetus. Sober writes:
One of the main objections to Darwin’s theory, both when the Origin was published and in the minds of many present-day Creationists, is the idea that species (or ‘‘fundamental kinds’’ of organism) are separated from each other by walls. No one doubted, then or now, that natural selection can cause small changes within existing species. The question was whether the process Darwin described can bring about large changes. Maybe a species can be pushed only so far. ...
If we focus just on natural selection, it is hard to see why Darwin had the more compelling case. However, if we set natural selection aside and consider instead the idea of common ancestry, the picture changes. Darwin thought he had strong evidence for common ancestry. This is enough to show that insuperable species boundaries (and insuperable boundaries between ‘‘kinds’’) are a myth; if different species have a common ancestor, the lineages involved faced no such walls in their evolution. And the case for common ancestry does not depend on natural selection at all. ...
Two of the facts mentioned earlier--that humans and monkeys have tailbones, and that human fetuses and fish have gill slits--are evidence for common ancestry precisely because tailbones and gill slits are useless in humans.
Sober goes on to explain that such "useless" designs make separate ancestry unlikely, and therefore make common ancestry likely. Evolution relies on this form argument and so Sober calls it Darwin's Principle. But Sober mysteriously fails to finish the story. Yes, such arguments are powerful, and they do make common ancestry a no-brainer. And they are ubiquitous in the evolution genre. But as with Gould's argument about why the panda's thumb proves evolution, they are religious.
Sober knows that Darwin's Principle is foundational to evolutionary claims. But amazingly he departs from his earlier thinking, where he criticized Gould for using religious assumptions, and now attempts to portray Darwin's Principle as metaphysically neutral. He explains that for "useless" designs, the likelihood ratio (the ratio of the probability of the design on common ancestry to the probability of the design on separate ancestry) is large because the denominator (the probability of the design on separate ancestry) is so small.
But Sober mysteriously fails to explain the obvious. The elephant in the room is ignored as Sober moves on to an analogy about term papers. The reason the denominator is so small is that a religious premise about divine intent was smuggled in. The reason those creationist concerns about insuperable boundaries do not hold is because common ancestry is likely. And common ancestry is likely because nature's designs given separate ancestry is unlikely. And those designs given separate ancestry are unlikely because god would not have given us our "useless" tailbones.
How ironic. The supposedly scientific theory of evolution relies on religious assumptions about divine intent to rebuke the religious theory of creation about its concerns that empirical observations indicate biological variation is limited.