Because if they don't come from God atoms and molecules would either be self existing or from the singularity.
Or formed by more basic particles. \
Molecules are made of atoms.
Atoms are made of protons, neutrons, and electrons.
Protons and neutrons are made of quarks.
Quarks and electrons, as far as we know, are not 'made of' anything more basic.
But they can be created and destroyed by any number of processes.
I believe the Bible because we are not sinners by stopping sin that is sinless perfectionism. The Bible says that the heart of people is desperately wicked.
OK, so that is one viewpoint.
Why would nature create everything if the universe is not eternal?
Huh? I'm not seeing the issue. Why would being eternal have anything to do with forming everything?
Nature creating everything would be pantheism and it's also vague. Nature cannot have an imagination.
And if it doesn't, what is the difficulty?