It seems to me like Eagleman seemed to believe his own argument is about the content of the debate, when it’s really more about tone. His point about Science’s institutional lack of certainty on certain questions is well- taken, but I wouldn’t say that’s at odds with what any of the New Atheists are saying. What the NAs are doing is basically dismantling religious claims using a variety of tools - scientific, philosophic, etc. There are certain points of contention in this debate that science actually has settled, and others where we have concluded that events did NOT occur the way that certain holy books tells us they did. And my point is, it’s not problematic to express “certainty” on these points.
The tone of the debate might lend one the impression that it is about two sides expressing undue “certainty,” but it really isn’t. The rationalist/scientific side of it comes with its own built-in rigors of intellectual honesty that all the participants know about. It’s not breaking rules or pressing an unfair advantage to claim (with accompanying evidence) to know how certain things happened, or to know how certain things didn’t happen.