Though modern science has led us to a great many discoveries about the nature of nature, it has not and cannot reach beyond the boundaries of nature and prove or disprove that which is super-natural. The fact is that the choice of concluding there is or isn't a God is one based solely on faith. Reason alone cannot lead to the denial of the miraculous.
Miracles are an integral part of the scriptures. The pages of the Bible of full of accounts where God acted within creation in supernatural ways - ways that nature itself could not act. To separate miracle from the Bible is to rid it of all divine nature altogether. A denial of miracle is denial of God.
Miracles by definition should be something that make us hyper-aware that things are not operating on a normal, natural level. When Jesus did a miracle, those who witnessed it were radically changed, even when the miracle was as seeming mundane as catching fish.