However, if the question "where do the atoms come from" is asked, then chemistry is not able to answer that question.
This might be true, but it is of no real consequence. Chemistry is just specialized physics, and physics can provide an answer to where atoms come from.
Under a government which imprisons any unjustly, the true place for a just man is also in prison. The proper place to-day, the only place which Massachusetts has provided for her freer and less desponding spirits, is in her prisons, to be put out and locked out of the State by her own act, as they have already put themselves out by their principles. Thoreau: Civil Disobedience (1846)