The instant a theist claims a real effect of god in the observable world, god becomes grist for the scientific mill. God is simply then an hypothesis for a causitive agent. You state that god caused thus and such (weather, healing, earthquakes, answering of general purpose prayers, etc...). The causes of these claims can be tested against our knowledge of nature. In no instance is any conclusion reached other than that the known phenomena of gravitation, thermodynamics, plate tectonics, and the "enumeration of favorable events" explain these things with great success. In addition, concluding that "god did it" leads to no predictable outcomes.
Therefore the hypothesis of god as a causitive agent in the universe is scientifically disproven, one phenomenon at a time. God as commonly understood and with the attributes given him by theists has been disproven, scientifically, time and again such that the overwhelming weight of evidence is in itself, proof. Unequivocally. Fear and culture are the sticky glue that binds this concept to us like gum stuck to the bottom of societies shoe. It needs to be scraped off.