Pinker argues that science makes belief in God obsolete

Here.  Here we run up once again against the claim that science shows that materialism is true. But, does that mean that science could have shown something else to be true, that, had the evidence been difference, science would have told us that we have souls? If you argue that science shows that we don't have souls, then it seems to follow from that that it could have shown that we do have them. Yet, arguments in support of souls are often thrown out on methodological grounds.

Consider, for example, the subtitle of The Blind Watchmaker: Why the evidence of evolution shows a world without design. Does that imply that if science had found something else, it would have concluded that we have a universe that WAS designed? Otherwise, the evidence isn't doing anything, since by definition it couldn't have discovered evidence for design even if it had been there. Right?