As Sean Carroll notes, it is technically true (Hume and the problem of induction strike again!) that an immaterial soul exists and is outside the provability bounds, or investigation, of current science.
But, as he also notes, it's also technically true that the moon, or some part of it at least, could in fact be made of green cheese!
And, he makes the burden heavy by whipping out Dirac's electron interaction equation and then asking soul believers to explain, in the terms of that equation, or if not, by adding scientifically measurable terms to that equation, how a soul could interact with the brain.
That said, one could be an epiphenomenalist. Perhaps Adam Frank, to whom Carroll is replying, is. But, while not logically impossible, nor inductively disprovable in a narrow sense, an epiphenomenalist soul that totally mirrors brain activity while never interacting with it is even more ludicrous than a soul that does. It's not too much to claim that it's impossible for such a critter to have evolved. And a deity that made that sort of soul would be even more ... risible? ... than one who made an immaterial, but interactionist, soul.
That said, it is true that science hasn't come close to investigating everything; it's also true that logically, you can't prove the nonexistence of anything — it's the equivalent of dividing by zero.
But, realistically? ....
Perhaps, as Alva Noe notes, the idea of a soul's existence is incoherent, a thought that a Wittgenstein would have us unask or unthink.
Otherwise, like many religious/philosophical ideas that originated thousands of years ago, it sounds wonderful to a nonrational part of our brains. But, wondrousness and desirability don't make anything more real. Not souls, not pearly gates, not weight-reducing chocolate or other things.
Plus, it's like the conservative Christian story of how non-rebellious angels were "confirmed in their goodness" after Satan's rebellion. Why couldn't the Judeo-Christian god have done that for Adam's progeny? Or, if immaterial souls are so good then, like the angels, why weren't we created with just them?
And, while I'm focusing on Christianity, it's not just it as a religion. It's the metaphysical claims of religion in general. If they're so good, and there's a divinity that does care about us that much, why not give us that at the start?
Claiming we need to "grow" here on earth? Really? That claim is never made as something we need to keep doing, and to keep doing with psychological toil and anguish, in an afterlife.
I think most agnostics, and the majority of atheists, even, would like to see some version of some of the metaphysical promises of organized religion be true. But, again, wondrousness isn't reality-making.
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