The simple answer is that some things lie outside the realm of science, but it does not make them any less important.
For example, questions such as 'why did the universe begin?', 'was there a specific purpose to it?', and 'was the cause of it a conscious being?', are all completely valid questions within the realm of philosophy, however they will probably never have any empirical evidence, and so the issues lie outside of the subject of science, by definition. All that science tries to do is observe our universe, and try to provide models for it, and to some extent explain it.
It does depend on how you define the concept of God though, and hence the concept of atheism; for some definitions science is incompatible, for others it is compatible.
Science is not compatible for a view of God in which God was said to have done real, objective things, for which there is much empirical evidence that such things were false. For example, the Christian God was said to have created the Garden of Eden and humans on the sixth day of creation. However science tells us through archaeological records that this is not true; there is no garden of Eden, and Earth was created a long time before humans appeared. Therefore the literal Christian God is not compatible with science, nor are the other classical Gods who supposedly did things which are not true. In that sense theism is not compatible with science.
However for some other ideas of God, such as a conscious creator of our universe (conscious perhaps being only a rough human definition of the true nature of that creator), there is certainally no empirical evidence suggesting that this is not true. Most people I think would agree that there is more to the whole of existence than just this universe, from the Big Bang onwards. That leaves fundamental questions unadressed, namely 'why?'; 'why not nothing?'.
In fact I would say that there is evidence for the existence of a cause that had an intent to create consciousness. There has been much criticism from rational people of the intelligent design argument, mainly because the logic takes the absurd leap from 'there is a God' to 'therefore there was the garden of Eden and Moses and Jesus etc. etc. because it says so in this book'.
However, I find it hard to believe at the current time that all of the cosmological constants and such were simply coincedences. Taking consciousness to be a result of the activity of neurons, just consider all of the separate elements which are vital for such a system to arise. You need a reality with matter. This matter must have extremely specific behaviours, which are the results of the sizes and shapes of electron orbitals, on the biological scale, in order to create the conditions in which organic molecules form spontaneously, and have the right materials, such as water and phospholipids for example, at hand. You need a universe with a huge number of habitat ranges (meaning planets with various temperatures and elements etcetera), by which I mean planets, for any hope that the whole system of evoultion will even start. And that's not even touching on the various constants which hang in an incredibly delicate balance such as the proportions between the different forces for there to be any useful matter to start off with. And all these probabilities cumulate to give what seems to be a miniscule probability that the consciousness could have arisen by coincedence.
All that remains is to ask yourself the question, 'why all this instead of nothing', and the idea that there is some purpose to the universe, namely conscious experience, kind of falls out freely. Purpose implies intent, and intent implies consciousness itself. So, for this definition of God (and I think there are probably others), theism is compatible with science.
Would you agree?
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