Your friend is very thoughtful and sounds more fair minded than many folks I have spoken to. The last quote that he recounts is especially apt to any quest to find scientific proof for God. The existence of God is what some philosophers (such as Alvin Plantinga) call a basic belief, part of an epistemological (knowledge) foundation upon which all our other beliefs are constructed.
There are people who interpret all of reality without the presupposition that God does exist (and is whom He describes Himself to be through Scripture); and there are those who do hold this foundational belief.
Foundational beliefs as such cannot be proven, but belief in God is only one example, there are many others such as those necessary for scientific endeavors. These include beliefs such as: that the structure of the world is rational and logical, that empirical observations can be trusted, that scientific methods in some way cohere to reality “as it truly is”.
Perhaps the best “scientific” argument for the existence of God is to ponder the question whether we have sufficient reason to believe (without proof) in the validity of our sense perception and rationality in a universe where there is no explanation for why there would be any order at all. Implausible tenets of the atheistic belief system include the idea that life came from non-life, order came from chaos, intelligence from an utter absence of thought, simply put, what we experience actually came from nothing (or alternatively, from an eternal lump of matter).
However, to posit that God does in fact exist, and remains the designer and sustainer of all that He made seems to me to provide the only possible answer to the problems raised above. If God did not exist, we would not live in a world like this, in a world where the basic methods of the sciences have a rational order and explaination- but we do in fact have a rational God.
A great article along these lines by the philosopher Alvin Plantinga called, An Evolutionary Argument against Naturalism. You can hear a great audio summary of this (where he says, “as far as I know there has never been a Calvinist Pope” about six times:
hisdefense.org/OnlineLectures/tabid/136/Default.aspx
A very long revamping of the original article is available here:
calvin.edu/academic/philosophy/virtual_library/articles/plantinga_alvin/naturalism_defeated.pdf