Though we may invoke God or enlightened beings for support, that I think is only one aspect of prayer–the other part is the whole dynamic of continually trying to orient yourself towards God (I can’t avoid putting it in these terms) and striving for a purposeful existence, to become more loving, compassionate, open, humble and less selfish. To stop trying to cut the corners in short. The wholeness (or holiness if you like) that comes from this is healing and leads to more harmonious and balanced living (if a great deal of our literature isn’t to be dismissed as either delusional or ingenuous).

This I think makes prayer tremendously rational, whatever the sterile metaphysical arguments. It is only inside this process that you can start to make any meaning of terms like ‘God’ and ‘Buddha nature’ and so forth, just as it is only when you start doing proper science that you can come to a proper understanding of terms like ‘work’, ‘light’, ‘gravity’ qua scientific concepts.

Also like science (and anything worthwhile),as Haim says, we should expect prayer to be a tremendously challenging process with its full share of traps and pitfalls and wrong turns. I don’t understand why it isn’t efficacious.

While I agree that science can’t make any sensible statements about God, the soul or say much meaningful on religious matters, Bishop Berkeley did identify the materialistic impulse of science–if allowed to progress unchecked as a serious threat to religious practice and formulated his idealistic philosophy in response. He said in famous passage in ‘A Treatise Concerning the Principles of Human Knowledge’, SS6:

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Some truths there are so near and obvious to the mind that a man need only open his eyes to see them. Such I take this important one to be, viz., that all the choir of heaven and furniture of the earth, in a word all those bodies which compose the mighty frame of the world, have not any subsistence without a mind, that their being (esse) is to be perceived or known; that consequently so long as they are not actually perceived by me, or do not exist in my mind or that of any other created spirit, they must either have no existence at all, or else subsist in the mind of some eternal spirit—it being perfectly unintelligible, and involving all the absurdity of abstraction, to attribute to any single part of them an existence independent of a spirit[1]. To be convinced of which, the reader need only reflect, and try to separate in his own thoughts the being of a sensible thing from its being perceived.
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As I said in a comment on Computers on the Brain, it took until the early 20th century for physics to catch up with the Bishop and realise that there is an inescapably and irreducibly ideal (mental) dimension of our existence. Many philosophers and scientists in the early 21st century have still to catch on though.