Unfortunately, science can analyze, describe, explain and confirm phenomena which exist only in the empirical natural world. Science, so far, cannot enter the supernatural world. If the supernatural world exists, science cannot come into this world to substantiate whether gods exist or not. In relation to the belief maintained by atheism that gods, and thus the supernatural world, don’t exist, science cannot substantiate either whether the supernatural world doesn’t exist.
We all know that our mind sometimes fails to recognize a reality due to our wrong perceptions or our lack of sufficient knowledge. So it could happen that we erroneously perceive something which actually exists to be something which doesn't exist, and the other way round. This means that the supernatural world which we empirically perceive as non-existent can possibly exist and we can confirm its existence if our mind has much more power and capacity to perceive more broadly and deeper and our sciences have developed and advanced far beyond their present state.
The recent advancement in Quantum physics leads us to the scientific knowledge we never have previously. Due to the contribution of, e.g., Max Planck and David Bohm, we presently know that particles in the Quantum world have both “proto-consciousness” or “free will” (as the wave aspect of a particle) and matter (as the matter aspect of a particle). This makes us realize more and more that matter and non-matter intermingle in the subatomic world. After pondering on this knowledge for a long time, I see the probability that perhaps one day in the future science will have the evidence that the natural and the supernatural worlds actually intersect. The transcendent and the immanent probably partly overlap. Perhaps our science will finally discover that the supernatural or the transcendent is the non-matter dimension of the universe as a whole. Our universe will still exist billions of years from now. Our science will make progress limitless. Countless generations of scientists in the future will open the "gates of heavens" that perhaps are still closed now, to attain new exciting scientific knowledge. Open mind is the only correct response to this exhilarating future.
In short, we cannot be absolutely sure that the supernatural world doesn't exist. The important thing is this: to be able to verify or to falsify the existence of gods in the supernatural world, science first has to enter this world to check―alas this is what our current science cannot do, as yet. In conclusion, if science is asked to substantiate the existence or the non-existence of gods, science presently cannot answer altogether. Science cannot prove or disprove the existence of gods.
Consequently, the strongest position concerning the existence of gods is to say that we currently cannot know absolutely whether gods exist or not. This position is known as agnostic position. The famous cosmologist and astronomer, the late Carl Sagan, refutes both atheism and theism, and chooses to become agnostic. Sagan very clearly presents his reasons why he opts for the agnostic position. In his book Broca’s Brain, he writes this:
“Those who raise questions about the God hypothesis and the soul hypothesis are by no means all atheists. An atheist is someone who is certain that God does not exist, someone who has compelling evidence against the existence of God. I know of no such compelling evidence. Because God can be relegated to remote times and places and to ultimate causes, we would have to know a great deal more about the universe than we do now to be sure that no such God exists. To be certain of the existence of God and to be certain of the nonexistence of God seem to me to be the confident extremes in a subject so riddled with doubt and uncertainty as to inspire very little confidence indeed. A wide range of intermediate positions seems admissible, and considering the enormous emotional energies with which the subject is invested, a questioning, courageous and open mind seems to be the essential tool for narrowing the range of our collective ignorance on the subject of the existence of God.”/1/
We know very well that religions employ many metaphors to describe various things so that religious people can understand religious things. A metaphor is a linguistic medium humans use to express in daily human languages things that are inexpressible or inexplicable so that most of the people can grasp and understand these things. Jesus of Nazareth as well as Gautama Buddha and other holy figures of the past use many metaphors when they communicate their convictions regarding the human life and other things that are beyond human and worldly daily life.
The message from me to atheists is therefore that they should not be trapped and imprisoned forever in the ontological debates about whether gods exist or not. Instead, it is much better for them to feel happy and peaceful too if a religious person is happy, serene, kind, tough, strong, optimistic, merciful, friendly, due to the metaphors of gods that he or she holds. Why should they attack such a pious religious people? Why should he or she be treated as atheists’ enemy? Why do atheists not love him or her?
/1/ Carl Sagan, Broca’s Brain: Reflection of the Romance of Science (New York: Random House, 1974, 1979), p. 365.