Whether intentionality is emergent or not, I believe that Ellis makes a good point. There is no scientific understanding of conscious awareness or intentionality, and there will never be as long as science continues with its “self-referential incompleteness”.

A robot can be set up to make decisions. If equipped with enough information and the right programming a robot can appear to exhibit intention. But we know that a robot’s decisions are determined by its memories, its software, and possibly by a random number generator and that it has no conscious awareness of self. In fact, it has no “self”. A robot is nothing but an assemblage of parts, no more aware than a rock. In the same way, organic bodies appear to make decisions, but in the case of organisms those decisions might sometimes be guided by conscious awareness, something that no one understands.

I do think Ellis has some interesting thoughts on the matter of science and revelation itself.

In his piece The Thinking Underlying the New ‘Scientific’ World-views, he says

“Issues such as the existence of God lie forever outside the competence of science to adjudicate, although the weight of data and experience can influence one’s opinion.”

A very valid assertion I would suggest.

This argument is flawed for the following reasons:

It assumes intentionality is a physical property of the universe instead of an emergent one as you have stated.

It also assumes a deterministic universe. This is not really the case, because the reality is that a pseudo deterministic world emerges from quantum uncertainty.

The biggest flaw in this argument, although not necessarily a logical error is it doesn't give credit to the ridiculous complexity of the human brain. If you asked top neurologists how complete our understanding of the brain was, they would say things like "if our understanding was represented by a mile, we have traveled no more than an inch".

His observation that we can't determine the next experiment we will do is a valid one, but it can be accouted for in physics with a basic understanding of entropy and information. To over simplify here, things need to interact with other things before they can know of the others existence. Because we don't have complete information about the universe, we can never know everything about it, thus we can not know what the next experiment will be.

This argument is logicaly coherent but fundamentaly wrong because it doesn't grasp how actual causality works.