Principle among his objections are that Shanon repeatedly seems to see the Bible as a kind of real history, rather than a collection of myths and legends that may (or may not) have some distant grounding in actual events. Moses was clearly not a Shaman, the events probably never took place as described (or at all), and there are plenty of other explanations for what's being described. Nelson also downplays the claims for entheogen use in other middle eastern traditions.
Shanon also cherry picks his evidence. None of this rules out the possibility that entheogens were used by the Israelites and influenced their mythic stories, but the positive evidence is pretty slim:
In the end his approach and the outcome mirror the research of scholars who over analyze and cherry pick the bible to find evidence of aliens in theophany. I certainly do not mean to say that there is no possibility that the Israelites used entheogens, but that there is at present no archaeological evidence and textual evidence is questionable at best.One of Shanon's hypotheses that is testable is his idea that acacia tree roots from the Sinai, when mixed with harmal (a shrub), produces a hallucinogenic brew. He doesn't seem to have tested this himself (although he has tested a similar concoction using a Brazilian acacia species.
It seems like a simple way to check his theory. Any volunteers?