i think atheism has merit from many different starting points (im referring to the abrahamic idea of God and all of the metaphysical baggage that goes with that world view). If we start at the biggest picture imaginable (outside of time, viewing what simply "is"), at the smaller picture (our own tiny perception of everything through our own consciousness), or in the middle (how we got here), it all leads to a naturalistic conclusion.
1. Philosophy/Physics: the idea of everything needing a cause relies on the fact that our brains our constructing a view of causation from WITHIN time. In reality, time is a 4th dimension and is only different from the others in that it is symmetry breaking. We perceive cause and effect because our brains can only make sense of a symmetry breaking dimension via "simple --> complex", "components-->more complex" sort of way. Outside of time, the time-space continuum just "sits there", and has no cause or beginning, because causation is a temporal idea.
2. science in the form of neuroscience/AI:
-human consciousness can in theory be accounted for without a "soul". Consciousness is basically the sensation of perceiving yourself to be thinking. The reason computers cant replicate ourselves is because computers are basically turing machines (010101010) and animal brains are anolog, parallel processing, neural net computer. If we could design a machine/software that could...
a. be dynamic rather than static (be able to change the very way its even written)
b. accumulate knowledge about itself (by remembering its responses and responses of others)
c. built in desires or simulated interests (things that the machine would want to ask about)
d. rules for spontaneity and randomness (so that it could comply with "do something new")
e. a mechanism for changing 'b', 'c' and 'd' in response to what 'b' collects.
f. capable of learning new skills and writing new software for itself (ie: learn how to speak a new langauge)
g. the ability to build virtual models, run models, and then adjust its skills, methods and conclusions accordingly.
the fact that such a machine is currently sci-fi is not important. whats important is that the machine we just described would for all intensive purposes be a person: it would have desires, memories, interests, creativity, and the ability to reason, learn, develope and evolve in response to its environment.
consciousness as such could then be, in theory, the result of an analog, parallel processing, neural net computer. Without spiritualism, the idea of god again becomes doubtful.
3. science in the form of biology:
evolution is practically a fact, theistic abiogenesis followed by natural evolution doesnt make any sense. (it would mean that god had to intervene with what was otherwise a universe made NOT for life...) secondly, evolution doesnt really work for the idea of souls...
4. science in the form of physics/math:
-intelligence can arise from non intelligence through randomness in up to 500 bit leaps. even creationist william dembski admits this with extensive math.
-order can arise from non-order via natural process: the planets arrange themselves due to gravity, which is a fundamental property of mass bending space-time (ie its the result of mindless geometry of space-time)