Thing is, on one level, I think Alpert is correct. Because we are self-reflectively aware and know that we will die, some degree of existential angst is unsurprising. That's quite probably a contributory factor to various human belief systems in which people can posit and believe in the eternal nature of human essence or soul. I feel reasonably sure that many people are believers for the very reason he states: they want to create for themselves some kind of assurance of personal eternality.
That said, just because some, or even many, people do that doesn't constitute proof that there's nothing to eternality, or more generally, what many think of as "spirituality". If one is prepared to look at such questions using the scientific method (which despite what Alpert asserts, goes on in a number of academic and other serious settings), the fact is, many of the bedrock assumptions of materialism are being tested.
He seems to me to be a naive realist, implicitly believing in the literal reality of what his senses tell him. For him, there really is a world out there that is exactly how it appears to be. The brain really is just a collection of material stuff arranged in a certain manner, out of which there really does emerge, in some as-yet unfathomable way, consciousness.
That's his free miracle: the one assumption he can't seem to truly question. Things are exactly and only what he perceives them to be, or what those in authority tell him he should perceive them to be (few of us are credentialled physicists and understand things in the same way they do at extreme scales -- either microscopic or macroscopic). The biggest thing he has going for him is that thinking in such a way is what enables us to engineer things that actually seem to work - everything from wheels to Hadron colliders. How could they all work in reliable and predictable ways unless what seems material is the basis for everything?
All over the place, in many different scientific areas, this largely received opinion is being questioned. The textbooks, however, continue to promulgate the view that the world is made of billiard balls that collide in various interesting ways even when the evidence mounts that correlation isn't causation. "Zombie science" as Jonathan Wells termed it in his book Zombie Science: More Icons of Evolution isn't just restricted to evolution: it permeates science as a whole.
Many of the people examining the tenets of materialism at the cutting edge, although they know it's questionable, still talk to the general public and even undergraduate and postgraduate students in terms of zombie science. It's good as dead, but still it walks around proclaiming it's alive and well. For whatever reason, though at least some scientists are aware of the limitations of the materialistic model of reality (and that's what in truth it is), it's a cultural imperative to tow the company line lest the scientific thought police get on your case and get you ostracised.
If materialists could at least accept in principle that materialism is just one way of modelling reality -- granted, a highly useful one in terms of empirical observations and engineering achievements -- and not necessarily reality itself, some kind of dialogue would be possible. But there are underlying ideological and metaphysical reasons why that isn't presently happening to any great extent, perhaps particularly (and somewhat ironically) in scientific areas quite far removed from physics. Many ardent materialists are quite often in the biological sciences, for example.
Either the universe is material, or materiality is an artifact of the way we perceive. The latter IMO is where Bernardo Kastrup and Donald Hoffman (amongst others) are coming from. If one's base assumption/free miracle is the former, then attempts to converse are unlikely to succeed, witness towards then end of the interview where Alpert, it seemed to me, was mostly positing as fact the very things that materialism asserts in order to prove itself. It's all very circular and it would be nice if there were some way to induce at least a scintilla of doubt.
Just getting a person like Alpert to at least intellectually understand and consider something like idealism, and how, if true, it could undermine his position, would be a major achievement. But for him it simply can't be so and so he won't really even consider the possibility. I have nothing personal against him, and in some respects his journey recapitulates my own, so I think I understand his take on things, but will he ever understand other viewpoints, or will he continue to kick the rock, like Samuel Johnson, thus refuting non-materialism?
Have to wait and see, but doesn't seem like there's much hope right now. My only plea would be for him to try to see materialism as a somewhat useful and successful model when it comes to adapting ourselves to reality as we perceive it, whilst retaining at least some skepticism/openness towards the possibility that appearances could be deceptive.