In a previous blog I spoke of the problem of evil, and how, perhaps it is the one major problem for Theism, but not necessarily Biblical Theism.
It's a common fallacy atheists commit when they usually ask, in the following form, or something very similar; "If God exists, why is the world such a mess, with disease, mutations, suffering. Why did He do such a bad job of things?"
Now the answer for this, biblically, is that God infact did NOT create most of these things. According to the bible, when mankind sinned, the earth was cursed, and the world was now in a fallen state, or a Godless state, whereby, all of the hallmarks of His design became tarnished over time.
If, however, you are solely Theist, and have no biblical beliefs, then the problem of evil is harder to address. Why is there suffering, and disease? Why is there killing, etc?
Can you see how the problem of evil, is logically more of a problem for a general Theism, rather than a Biblical Theism?
Another example of God having a tarnished reputation in atheists' sight, is design, and the problem of conflating design with degredation and degeneration of the world. Harmful mutations, disease, are all intepreted by the atheist, to be the result of coming directly from God's creative hand for the PURPOSE of attacking humans, and causing suffering.
It cannot be further from the truth, in the sense that God's motivations were never to create such things to harm us, but they were originally created for a symbiotic existence. All of the creatures, AT the time of creation, would have be symbiotic. i.e. Living in a mutually beneficial relationship to all other creatures, etc, or complimenting one another.
For example, the components of your garden are created to compliment the various other components, aesthetically, or practically etc...
It's hard to fully understand how this could have been so, but if the world is in a fallen state, then it is very hard to imagine a previous time, where things were very different. A little bit like imagining living in a sunny climate, if you have only ever known arctic conditions.