Can you explain the difference between scientific and non-scientific research?

Joe says, “I don’t believe in God, because there’s no evidence.”

Ben says, “I believe in God because there’s all the evidence in the world! The blind have been healed! The paralyzed walk! The dead were brought back to life!”

Joe says, “I’m pretty well-read, and science has not discovered anything of God.”

Ben says, “You read your books, I’ve read mine, and the Bible says there’s a God. It’s all just opinions in books.”

Joe says, “I’ve tried to disprove my atheism through research, and failed.”

Ben says, “I did my research in the Bible, and the Bible says there’s a God. I tried to disprove my theism, and failed.”

Question for you folks: Both Ben and Joe believe they have done research, but I would argue that there’s an essential difference in what they have both done. If you agree with me, how would you describe the difference?

I’m not looking for a religion/atheism fight, or putdowns. I’m not looking to prove God or religion true or false. I’m looking for a way to explain the essential difference between the sorts of research that they have both done. Thank you!