Here, from a letter to an atheist:
Science brings men nearer to God.
Posterity will one day laugh at the foolishness of modern materialistic philosophers. The more I study nature, the more I stand amazed at the work of the Creator. I pray while I am engaged at my work in the laboratory.
The Greeks understood the mysterious power of the below things. They are the ones who gave us one of the most beautiful words in our language, the word enthusiasm: a God within.
I have been looking for spontaneous generation for twenty years without discovering it. No, I do not judge it impossible. But what allows you to make it the origin of life? You place matter before life and you decide that matter has existed for all eternity. How do you know that the incessant progress of science will not compel scientists to consider that life has existed during eternity, and not matter? You pass from matter to life because your intelligence of today cannot conceive things otherwise. How do you know that in ten thousand years, one will not consider it more likely that matter has emerged from life? You move from matter to life because your current intelligence, so limited compared to what will be the future intelligence of the naturalist, tells you that things cannot be understand otherwise. If you want to be among the scientific minds, what only counts is that you will have to get rid of a priori reasoning and ideas, and you will have to do necessary deductions not giving more confidence than we should to deductions from wild speculation. [en francais, Pasteur et la philosophie, Patrice Pinet, Editions L’Harmattan, p. 63.]