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Does science justify atheism?
Science works on certain assumptions, one of the key assumptions is positive evidence justifies positive claims. In the absence of positive evidence no claim should be made.
As there is no positive evidence for any particular belief/system no claim, or Atheism, is justified.
It is scientifically justified to abstain from making a claim that a god exists when there is insufficient evidence upon which to base a claim that any such god exists.
Atheism is an assertion that no deity exists - of course it needs to be justified. Especially since science admits that it cannot prove a universal negative.
Positive evidence for a claim might not be scientific. It could be philosophical, mathematical, or experiential.
The limitations of human cognitive abilities, relative to assumptions being weak and fundamentally flawed, produces the uncertainty factor that promotes faith-based assumptions to fill in gaps of knowledge inherently present among the evidence within science.
This is the same as saying that science has starting assumptions that aren't compatible with the types of claims religion makes. If the difference is that foundational, there is no strong reason to prefer either set of arbitrary commitments, per Lyotard.