Can prayer change God's perfect plan?

[Fake Messiah]

God wants us to protect ourselves.

Hey, we want to protect ourselves. That is what people are trying to do with science, like medicine. This is the reason why hospitals aren't staffed with shamans and preachers rather than doctors and nurses. If prayer healing really worked wouldn't we all be relying on it by now? But what when belief in god negatively impacts world peace, the education of children, the development of new medical cures, safety and justice for women, and the progress of science?

I bet when you said "God wants us to protect ourselves." you didn't mean we should educate people in Africa to use contraception to avoid AIDS? Or that we should pursue more stem cell research that have enormous potential for curing human diseases, regrowing tissues and organs, and attacking a variety of previously intractable medical problems like Alzheimer's disease, Parkinson's disease, and spinal cord injuries. Or when earthquake happens and kills hundreds of thousands of people should we invest more in punishing people for homosexuality and non belief in god or more investing in science of detecting earthquakes in time to save lives?
Or what do you think about pressure from the Catholic Church has also halted the administration of anti-HPV vaccines in Trinidad and Tobago, with the church going so far as to question, in the face of all scientific fact, the safety of the vaccine. This is clearly "not helping ourselves" - wouldn't you say?

Some people like to think that every little thing that happens was purposely made to happen by the hand of God Himself.

But what abut big things, like virus of malaria; or dysentery; or hurricanes? Who made that? And if wasn't by god why couldn't he stop it? Why should innocent people die in hundreds of thousands? Or what about fact that more than a billion people do not have access to safe drinking water? Or that about half of the world's children live in severe poverty? - I mean what am I missing here? Are those "little things"?
God does as he wishes, no matter how irrational or disproportionate.

Even if you insist that anything god does is good by definition. Still, the effects down here on earth are the same: pain, misery, and strife imposed on innocent and guilty alike, under the apparent indifference, neglect, or even intentional cruelty of this powerful good god. If such a god really does exist, it's hard to accept how he deserves our praise.

He created this world with us in it and allows nature to happen as it will, and allows us to make our own choices.

So he gave us free will and that explains it? Why, for instance, did God, who should have known better, make such a flawed creature as man, who would likely if not certainly use his free will to his own detriment? If you believe God is omnipotent is it not logical to conclude that he could have made an improved human who still possessed free will - one who was more likely to choose freely the course of good. Here's an analogy: when people as parents raise good children, children who are more prone to act morally and positively, they have not thereby taken away their free will.