John Polkinghorne believes that prayer is more than just wishful thinking. He offers three observations to the contrary-- one scientific, one human, and one religious.
First, the scientific reason-- the world is not a predictable mechanism. The universe operates in a more subtle way than simply as a large always predictable clock. Polkinghorne offers the weather as an example as it is "incredibly complicated, in a way that makes it impossible to say exactly what will or will not make it rain next Saturday" (Quarks, Chaos, and Christianity, pp. 80-81). The smallest and most unpredictable events can have large consequences in our world and universe.
Second, the human reason-- "we didn't actually need modern science to tell us that it's not all mechanical, for we've always known-- as sure as we know anything-- that we are not automata" (p. 81).
Human beings truly have choice and the universe can act in random fashion. If human beings can truly act in a way that the future can remain open, then is it unreasonable to think that God can act in the midst of his creation as well?
Third, the religious reason-- Christianity, Judaism, and Islam all speak of God in personal terms. God is not a force or an abstract and impersonal higher power. Thus if God is personal and cares for his creation, does it not seem logical that God could and would act in it and also hear our prayers and respond? "The Creator is not just the God of the whole big show, but also the God of Abraham, Isaac, and Jacob, of you and me. Such a God must be able to do specific things. The laws of nature (which, after all, are themselves just general expressions of the will of the faithful Creator) cannot be such as to prevent divine interaction with creation" (pp. 81-82).
Polkinghorne will explore in greater detail the matter of uncertainty and predictability as a way of suggesting that God can and does answer prayer.
...in part 3.
Can a Scientist Pray? (Part 1: Introduction)